Previous changeset 6:b2967b704d6b (2023-05-23) Next changeset 8:0966b9635d76 (2023-06-14) |
Commit message:
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0736f8541b223428139cbc9403c4db591b324280 |
modified:
frogsfunc_functions.xml frogsfunc_pathways.xml frogsfunc_placeseqs.xml macros.xml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
added:
test-data/databases/frogs_picrust2_functions.loc test-data/databases/frogs_picrust2_pathways.loc test-data/databases/frogs_picrust2_placeseqs.loc tool-data/frogs_picrust2_functions.loc.sample tool-data/frogs_picrust2_pathways.loc.sample tool-data/frogs_picrust2_placeseqs.loc.sample |
removed:
test-data/1683127225.892718_18537_mafft.stderr test-data/1683127225.892718_18537_mafft_aligned.fasta test-data/1683188955.2635202_141707_rmarkdown.stderr test-data/1683615440.2244859_24853_R.stderr test-data/1683615471.1625206_25567_R.stderr test-data/1683618354.3833234_48737_cleaned.fasta test-data/1683618354.3833234_48737_tmp_convert_fasta.log test-data/1683618354.3833234_48737_tmp_place_seqs.log test-data/1683619172.2099853_50503_cleaned.fasta test-data/1683619172.2099853_50503_tmp_convert_fasta.log test-data/1683619172.2099853_50503_tmp_place_seqs.log test-data/1683625674.1083791_56412_genes_abundances_formatted.tsv test-data/EC_copynumbers_predicted.tsv test-data/affi-filterd.log test-data/affi-stats.log test-data/affiliation_abundance.biom test-data/affiliation_filters.test.log test-data/all_tool_test_output.html test-data/asv_data.Rdata test-data/asv_dds.Rdata test-data/biom_to_tsv.log test-data/chaillou.tsv test-data/cluster_filters.log test-data/cluster_stats.log test-data/databases/frogs_picrust2_default_dir.loc test-data/databases/frogs_picrust2_marker_table.loc test-data/databases/frogs_picrust2_pathway_map.loc test-data/deseq_peepro.log test-data/deseq_visu.log test-data/deseq_visu_2.log test-data/filters.tsv test-data/frogsfun test-data/frogsfunc.tsv test-data/frogsfunc_function.biom test-data/frogsfunc_function.fasta test-data/frogsfunc_function.log test-data/frogsfunc_pathways_predictions.tsv test-data/frogsfunc_pathways_strat.tsv test-data/frogsfunc_pathways_summary.html test-data/frogsfunc_pathways_unstrat.tsv test-data/frogsfunc_pathways_unstrat_per_seq.tsv test-data/frogsfunc_placeseq.log test-data/log_chimera.txt test-data/log_cluster_filter.txt test-data/log_clustering.txt test-data/log_itsx.txt test-data/log_itsx_2.txt test-data/log_preprocess.txt test-data/multihits.tsv test-data/phyloseq_alpha_diversity.nb.html test-data/phyloseq_alpha_diversity.tsv test-data/phyloseq_beta test-data/phyloseq_beta.log test-data/phyloseq_import.log test-data/phyloseq_manova.html test-data/phyloseq_manova.nb.html test-data/planemo_test.log test-data/planemo_test.sh test-data/planemo_test_2.log test-data/planemo_test_3.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.lint.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.test.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.lint.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.test.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.lint.log test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.test.log test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.lint.log test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.test.log test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.lint.log test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.test.log test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.lint.log test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.test.log test-data/planemo_test_4.1.0_vincentdarbot/cluster_stats.lint.log test-data/planemo_test_4.1.0_vincentdarbot/clustering.lint.log test-data/planemo_test_4.1.0_vincentdarbot/clustering.test.log test-data/planemo_test_4.1.0_vincentdarbot/demultiplex.lint.log test-data/planemo_test_4.1.0_vincentdarbot/deseq2_preprocess.lint.log test-data/planemo_test_4.1.0_vincentdarbot/deseq2_visualisation.lint.log test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_functions.lint.log test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_pathways.lint.log test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_placeseqs.lint.log test-data/planemo_test_4.1.0_vincentdarbot/itsx.lint.log test-data/planemo_test_4.1.0_vincentdarbot/macros.lint.log test-data/planemo_test_4.1.0_vincentdarbot/normalisation.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_alpha_diversity.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_beta_diversity.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_clustering.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_composition.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_import_data.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_manova.lint.log test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_structure.lint.log test-data/planemo_test_4.1.0_vincentdarbot/preprocess.lint.log test-data/planemo_test_4.1.0_vincentdarbot/remove_chimera.lint.log test-data/planemo_test_4.1.0_vincentdarbot/taxonomic_affiliation.lint.log test-data/planemo_test_4.1.0_vincentdarbot/tree.lint.log test-data/planemo_test_4.1.0_vincentdarbot/tsv_to_biom.lint.log test-data/planemo_test_4.log test-data/planemo_test_5.log test-data/planemo_test_6.log test-data/preprocess.log test-data/taxo_affi.log test-data/taxo_enrichment.tsv test-data/taxonomic_affiliation.log test-data/test/deseq2_preprocess.log test-data/test/frogsfunc_function.log test-data/test/frogsfunc_pathway.log test-data/test/frogsfunc_pathways.log test-data/test/frogsfunc_placeseqs.log test-data/test/preprocess.log test-data/test/taxo_affi.log test-data/tool_test_output_all.html test-data/tree.log test-data/tsv_to_biom.log tool-data/frogs_picrust2_default_dir.loc.sample tool-data/frogs_picrust2_marker_table.loc.sample tool-data/frogs_picrust2_pathway_map.loc.sample |
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diff -r b2967b704d6b -r f479218f3736 frogsfunc_functions.xml --- a/frogsfunc_functions.xml Tue May 23 07:59:04 2023 +0000 +++ b/frogsfunc_functions.xml Tue Jun 13 06:59:09 2023 +0000 |
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@@ -65,7 +65,7 @@ <!-- Parameters--> <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio"> - <options from_data_table="frogs_picrust2_marker_table"> + <options from_data_table="frogs_picrust2_functions"> <column name='name' index='0' /> <column name='value' index='0' /> <filter type="unique_value" column='0'/> @@ -73,7 +73,7 @@ </options> </param> <param argument="--functions" type="select" label="Target function database" multiple="true" optional="false" help=" 16S : at least 'EC' or/and 'KO' should be chosen (EC for Metacyc pathway analysis or/and KO for KEGG pathway analysis) - others values are optionnal. ITS and 18S : 'EC' only available." > - <options from_data_table="frogs_picrust2_marker_table"> + <options from_data_table="frogs_picrust2_functions"> <column name='name' index='1' /> <column name='value' index='1' /> <column name='path' index='2' /> @@ -146,7 +146,7 @@ <param name="input_biom" value="references/25-frogsfunc_placeseqs.biom" /> <param name="input_tree" value="references/25-frogsfunc_placeseqs_tree.nwk" /> <param name="input_marker" value="references/25-frogsfunc_copynumbers_marker.tsv" /> - <param name="category.value" value="frogs_picrust2_marker_table" /> + <param name="category.value" value="frogs_picrust2_functions" /> <param name="functions" value="EC" /> <param name="max_nsti" value="2" /> |
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diff -r b2967b704d6b -r f479218f3736 frogsfunc_pathways.xml --- a/frogsfunc_pathways.xml Tue May 23 07:59:04 2023 +0000 +++ b/frogsfunc_pathways.xml Tue Jun 13 06:59:09 2023 +0000 |
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@@ -43,7 +43,7 @@ <!-- References --> <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio"> - <options from_data_table="frogs_picrust2_pathway_map"> + <options from_data_table="frogs_picrust2_pathways"> <column name='name' index='2' /> <column name='value' index='2' /> <filter type="unique_value" column='2'/> @@ -51,7 +51,7 @@ </options> </param> <param name="map_file" type='select' label="Pathway reference" help="For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_1_placeseqs_copynumbers tool. For ITS or 18S marker, Metacyc is the only valid option." optional="false" multiple='false' display='radio'> - <options from_data_table="frogs_picrust2_pathway_map"> + <options from_data_table="frogs_picrust2_pathways"> <column name='name' index='1'/> <column name='value' index='3'/> <filter type="param_value" ref="category" column="2" /> |
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diff -r b2967b704d6b -r f479218f3736 frogsfunc_placeseqs.xml --- a/frogsfunc_placeseqs.xml Tue May 23 07:59:04 2023 +0000 +++ b/frogsfunc_placeseqs.xml Tue Jun 13 06:59:09 2023 +0000 |
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@@ -56,7 +56,7 @@ <!-- Parameters --> <param argument="--ref-dir" name="marker" type="select" label="Taxonomy marker" display="radio" help="Taxonomic marker of interest."> - <options from_data_table="frogs_picrust2_default_dir"> + <options from_data_table="frogs_picrust2_placeseqs"> <column name="name" index="1"/> <column name="value" index="2"/> <column name="traits" index="3"/> @@ -65,7 +65,7 @@ </options> </param> <param argument="--placement-tool" type="select" label="Placement tool" help="Placement tool for insertion of sequences into the reference tree. SEPP is a low-memory alternative to EPA-ng for placing sequences, and is only available for 16S analysis." multiple="false" display="radio"> - <options from_data_table="frogs_picrust2_default_dir"> + <options from_data_table="frogs_picrust2_placeseqs"> <column name='name' index='4' /> <column name='value' index='4' /> <filter type="param_value" ref="marker" column="2" /> |
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diff -r b2967b704d6b -r f479218f3736 macros.xml --- a/macros.xml Tue May 23 07:59:04 2023 +0000 +++ b/macros.xml Tue Jun 13 06:59:09 2023 +0000 |
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@@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">4.1.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <xml name="requirements"> <requirements> |
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diff -r b2967b704d6b -r f479218f3736 test-data/1683127225.892718_18537_mafft.stderr --- a/test-data/1683127225.892718_18537_mafft.stderr Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,1 +0,0 @@ -/bin/sh: 1: mafft: not found |
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diff -r b2967b704d6b -r f479218f3736 test-data/1683188955.2635202_141707_rmarkdown.stderr --- a/test-data/1683188955.2635202_141707_rmarkdown.stderr Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,2 +0,0 @@ -Erreur : pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available). -Exécution arrêtée |
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diff -r b2967b704d6b -r f479218f3736 test-data/1683615440.2244859_24853_R.stderr --- a/test-data/1683615440.2244859_24853_R.stderr Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,2 +0,0 @@ -Erreur dans library(DESeq2) : aucun package nommé ‘DESeq2’ n'est trouvé -Exécution arrêtée |
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diff -r b2967b704d6b -r f479218f3736 test-data/1683615471.1625206_25567_R.stderr --- a/test-data/1683615471.1625206_25567_R.stderr Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,110 +0,0 @@ -Le chargement a nécessité le package : S4Vectors -Le chargement a nécessité le package : stats4 -Le chargement a nécessité le package : BiocGenerics - -Attachement du package : ‘BiocGenerics’ - -Les objets suivants sont masqués depuis ‘package:stats’: - - IQR, mad, sd, var, xtabs - -Les objets suivants sont masqués depuis ‘package:base’: - - anyDuplicated, append, as.data.frame, basename, cbind, colnames, - dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, - grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, - order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, - rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, - union, unique, unsplit, which.max, which.min - - -Attachement du package : ‘S4Vectors’ - -Les objets suivants sont masqués depuis ‘package:base’: - - expand.grid, I, unname - -Le chargement a nécessité le package : IRanges -Le chargement a nécessité le package : GenomicRanges -Le chargement a nécessité le package : GenomeInfoDb -Le chargement a nécessité le package : SummarizedExperiment -Le chargement a nécessité le package : MatrixGenerics -Le chargement a nécessité le package : matrixStats - -Attachement du package : ‘MatrixGenerics’ - -Les objets suivants sont masqués depuis ‘package:matrixStats’: - - colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, - colCounts, colCummaxs, colCummins, colCumprods, colCumsums, - colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, - colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, - colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, - colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, - colWeightedMeans, colWeightedMedians, colWeightedSds, - colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, - rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, - rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, - rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, - rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, - rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, - rowWeightedMads, rowWeightedMeans, rowWeightedMedians, - rowWeightedSds, rowWeightedVars - -Le chargement a nécessité le package : Biobase -Welcome to Bioconductor - - Vignettes contain introductory material; view with - 'browseVignettes()'. To cite Bioconductor, see - 'citation("Biobase")', and for packages 'citation("pkgname")'. - - -Attachement du package : ‘Biobase’ - -L'objet suivant est masqué depuis ‘package:MatrixGenerics’: - - rowMedians - -Les objets suivants sont masqués depuis ‘package:matrixStats’: - - anyMissing, rowMedians - -Messages d'avis : -1: le package ‘DESeq2’ a été compilé avec la version R 4.1.3 -2: le package ‘S4Vectors’ a été compilé avec la version R 4.1.3 -3: le package ‘IRanges’ a été compilé avec la version R 4.1.3 -4: le package ‘GenomicRanges’ a été compilé avec la version R 4.1.3 -5: le package ‘GenomeInfoDb’ a été compilé avec la version R 4.1.3 -6: le package ‘matrixStats’ a été compilé avec la version R 4.1.3 -7: le package ‘Biobase’ a été compilé avec la version R 4.1.3 - -Attachement du package : ‘phyloseq’ - -L'objet suivant est masqué depuis ‘package:SummarizedExperiment’: - - distance - -L'objet suivant est masqué depuis ‘package:Biobase’: - - sampleNames - -L'objet suivant est masqué depuis ‘package:GenomicRanges’: - - distance - -L'objet suivant est masqué depuis ‘package:IRanges’: - - distance - -converting counts to integer mode -estimating size factors -estimating dispersions -gene-wise dispersion estimates -mean-dispersion relationship -final dispersion estimates -fitting model and testing --- replacing outliers and refitting for 19 genes --- DESeq argument 'minReplicatesForReplace' = 7 --- original counts are preserved in counts(dds) -estimating dispersions -fitting model and testing |
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diff -r b2967b704d6b -r f479218f3736 test-data/1683618354.3833234_48737_cleaned.fasta --- a/test-data/1683618354.3833234_48737_cleaned.fasta Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,20 +0,0 @@ ->Cluster_1 -TGGGGAATATTGGGCAATGGACGCAAGTCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTTGTAAACTTCTTTTGTCAGGGAACAGTAGAAGAGGGTACCTGACGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGCAGCCGGGCCGGCAAGTCAGATGTGAAATCTGGAGGCTTAACCTCCAAACTGCATTTGAAACTGTTGGTCTTGAGTACCGGAGAGGTTATCGGAATTCCTTGTGTAGCGGTGAAATGCGTAGATATAAGGAAGAACACCAGTGGCGAAGGCGGATAACTGGACGGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAAC ->Cluster_2 -TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAAC ->Cluster_3 -TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGTGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGAGTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAAGCAAGTCTGGAGTGAAAACCCGGGGCTTAACCCCGGGATTGCTTTGGAAACTGTTTAACTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC ->Cluster_4 -TGGGGAATATTGGGCAATGGAGGCAACTCTGACCCAGCAACGCCGCGTGAATGATGAAGGTCTTCGGATTGTAAAGTTCTGTGACGGGGGACGAACACAATGACGGTACCCCGATAGCAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTAGCAAGTTGGCAGCGTAATTCCGGGGCTCAACTCCGGCGCTACTGCCAAAACTGTTGAACTTGAGTGCAGGAGGGGTAAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACATCGGTGGCGAAGGCGACTTACTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAAC ->Cluster_5 -TGGGGAATATTGGGCAATGGAGGGAACTCTGACCCAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATTGTAAAACTCTTTAAGCGGGGACGAAGAAAGTGACTGTACCCGCAGAATAAGCATCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGATGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTGCCAAGTTGGCAGCGTAATTCCGTGGCTTAACCGCGGAACTACTGCCAAAACTGGTAGGCTTGAGTGCGGCAGGGGTATGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAAGCGACATACTGGGCCGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAAC ->Cluster_6 -TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAACTGACGGTACCTGACTAAGAAGCACCGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATGTGCAAGTCTGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTAGATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC ->Cluster_7 -TAGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGGAGGATGACACTTTTCGGAGCGTAAACTCCTTTTCTTAGGGAAGAATTCTGACGGTACCTAAGGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGGGCGCGTAGGCGGATTATCAAGTCTCTTGTGAAATCTAATGGCTTAACCATTAAACTGCTTGGGAAACTGATAGTCTAGAGTGAGGGAGAGGCAGATGGAATTGGTGGTGTAGGGGTAAAATCCGTAGATATCACCAAGAATACCCATTGCGAAGGCGATCTGCTGGAACTCAACTGACGCTAAGGCGCGAAAGCGTGGGGAGCAAAC ->Cluster_10 -TGGGGAATATTGGGCAATGGGCGCAAGCCTGACCCAGCAACGCCGCGTGAAGGATGAAGGCTTTCGGGTTGTAAACTTCTTTTATTCGGGACGAAGCAAGTGACGGTACCGAATGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGACTGCAAGTCAGATGTGAAAACTATGGGCTCAACCCATAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCATAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAAC ->Cluster_11 -TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCACCGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATAGGCAAGTCTGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTTTATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC ->Cluster_12 -TGGGGAATATTGGGCAATGGGCGCAAGCCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTTGTAAACTTCTTTTGTCGGGGACGAAACAAATGACGGTACCCGACGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGATTGCAAGTCAGATGTGAAAACTGGGGGCTCAACCTCCAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAAC |
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diff -r b2967b704d6b -r f479218f3736 test-data/1683618354.3833234_48737_tmp_place_seqs.log --- a/test-data/1683618354.3833234_48737_tmp_place_seqs.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,21 +0,0 @@ -hmmalign --trim --dna --mapali /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /tmp/tmpnhwfzlcm/query_align.stockholm /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm 1683618354.3833234_48737_cleaned.fasta - -Raw input sequences ranged in length from 401 to 426 - -run_sepp.py --tree /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpnhwfzlcm/sepp_out -seed 297834 --alignment /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpnhwfzlcm/study_seqs_filtered.fasta - -Error running this command: -run_sepp.py --tree /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpnhwfzlcm/sepp_out -seed 297834 --alignment /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpnhwfzlcm/study_seqs_filtered.fasta - -Standard error of the above failed command: -Traceback (most recent call last): - File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/bin/run_sepp.py", line 3, in <module> - from sepp.exhaustive import ExhaustiveAlgorithm - File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/exhaustive.py", line 6, in <module> - from sepp.algorithm import AbstractAlgorithm - File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/algorithm.py", line 11, in <module> - from sepp.tree import PhylogeneticTree - File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/tree.py", line 25, in <module> - from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ -ImportError: cannot import name '_convert_node_to_root_polytomy' - |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/1683619172.2099853_50503_cleaned.fasta --- a/test-data/1683619172.2099853_50503_cleaned.fasta Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,20 +0,0 @@ ->Cluster_1 -GACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGAACGGATAAAGAGCTTGCTCTTTTGAAGTTAGTGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCTCACAGCTGGGGATAACATCGAGAAATCGATGCTAATACCGAATGTGCTGAACATCATAAGATGTTCAAGTGAAAGACGGTTTCGGCTGTCACTGTGAGATGGACCCGCGCTGGATTAGCTAGTTGGTAAGGTAATGGCTTACCAAGGCGACGATCCATAGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGCGAAGAAGGCCTTCGGGTCGTAAAGCTCTGTTGTTAGAGAAGAACATGGGTGAGAGTAACTGTTCACCCCTTGACGGTATCTAACCAGAAAGCCACGGCTAACTACGTG ->Cluster_2 -ATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGGTAACAGATTGATAGCTTGCTATCAATGCTGACGAGCGGCGGACGGGTGAGTAATGCCTGGGAATATACCCTGATGTGGGGGATAACTATTGGAAACGATAGCTAATACCGCATAATCTCTTCGGAGCAAAGAGGGGGACCTTCGGGCCTCTCGCGTCAGGATTAGCCCAGGTGGGATTAGCTAGTTGGTGGGGTAATGGCTCACCAAGGCGACGATCCCTAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGTTGTGAGGAAGGCGTTGGAGTTAATAGCTTCAGCGCTTGACGTTAGCAACAGAAGAAGCACCGGCTAACTCCGTG ->Cluster_3 -GACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGCACTCTCGTTTAGATTGAAGGAGCTTGCTCCTGATTGATAAACATTTGAGTGAGTGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCCTAAAGTGGGGGATAACATTTGGAAACAGATGCTAATACCGCATAAAACCTAACACCGCATGGTGTAGGGTTGAAAGATGGTTTCGGCTATCACTTTAGGATGGACCCGCGGTGCATTAGTTAGTTGGTGAGGTAAAGGCTCACCAAGACCGTGATGCATAGCCGACCTGAGAGGGTAATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTGGAGAAGAATGTATCTGATAGTAACTGATCAGGTAGTGACGGTATCCAACCAGAAAGCCACGGCTAACTACGTG ->Cluster_4 -GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTGCTTTTGTGGGGTGCTCGAGTGGCGAACGGGTGAGTAACACGTGAGTAACCTGCCCTTGACTTTGGGATAACTTCAGGAAACTGGGGCTAATACCGGATAGGAGCTCCTGCTGCATGGTGGGGGTTGGAAAGTTTCGGCGGTTGGGGATGGACTCGCGGCTTATCAGCTTGTTGGTGGGGTAGTGGCTTACCAAGGCTTTGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCTGATGCAGCAACGCCGCGTGCGGGATGACGGCCTTCGGGTTGTAAACCGCTTTCGCCTGTGACGAAGCGTGAGTGACGGTAATGGGTAAAGAAGCACCGGCTAACTACGTG ->Cluster_5 -GATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGCACAGCGAAAGGTGCTTGCACCTTTCAAGTGAGTGGCGAACGGGTGAGTAACACGTGGATAACCTACCTCAAGGTTGGGGATAACATTTGGAAACAGATGCTAATACCGAATAAAACTTAGTATCGCATGATACCAGGTTAAAAGGCGCTACGGCGTCACCTAGAGATGGATCCGCGGTGCATTAGTTAGTTGGTGGGGTAAAGGCTTACCAAGACAATGATGCATAGCCGAGTTGAGAGACTGATCGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCTGCAGTAGGGAATCTTCCACAATGGGCGAAAGCCTGATGGAGCAACGCCGCGTGTGTGATGAAGGCTTTCGGGTCGTAAAGCACTGTTGTATGGGAAGAACAGCTAGAGTAGGGAATGACTTTAGTTTGACGGTACCATACCAGAAAGGGACGGCTAAATACGTG ->Cluster_6 -GACGAACGCTGGCGGCGTGCCTAATACATGCAAGTTGAACGATGATTTCTGGTACTTGTATCAGAATGAAGAGTAGCGAACGGGTGAGTAACGCGTGGGTAACCTACCTCTTAGCGGGGGACAACTATTGGAAACGATAGCTAATACCGCATAACAATGCTTAACACATGTTAAGCATTTGAAAGTACCAATTGGTACACTAGGAGATGGACCCGCGTTGTATTAGCTAGTTGGTAGTGTAATGGACTACCAAGGCGATGATACATAGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAGAGAAGAACGTTGTGTAGAGTGGAAAATTACACAAGTGACGGTATCTAACCAGAAAGGGACGGCTAACTACGTG ->Cluster_7 -GATGAACGCTGGCGGCATGCCTAAGACATGCAAGTCGAACGAGGGGACCCAACAATTATGAAGTACTTGTACGGATTATGCGATGGATTCACACCTAGTGGCGAACGGGTGAGTAACGGGTAGGCAACCTGCCCTCAAGACGGGGATACCAGTTGGAAACGACTGTTAATACCGGATAGTATACAATATCGCATGGTAATGTATTTAAAGGAGCTTCGGCTTCACTTGAGGATGGGCCTGCTTTGTATTAGATAGTTGGTGAGGTAATGGCTCACCAAGTCAACGATGCATAGCCGAACTGAGAGGTTGAACGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTTAGGGATATTGGGCAATGGAGGAAACTCTGACCCAGCAATGCCGCGTGAGTGAAGAAGTATTTCGGTATGTAAAACTCTGTTGTATGGGAGGAAAGAACTAGTAGGAAATGGCTAGGAG ->Cluster_8 -GACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGATGATTAAAGATAGCTTGCTATTTTTATGAAGAGCGGCGAACGGGTGAGTAACGCGTGGGAAATCTGCCGAGTAGCGGGGGACAACGTTTGGAAACGAACGCTAATACCGCATAACAATGAGAATCGCATGATTCTTATTTAAAAGAAGCAATTGCTTCACTACTTGATGATCCCGCGTTGTATTAGCTAGTTGGTAGTGTAAAGGACTACCAAGGCGATGATACATAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGGGGCAACCCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAGAGAAGAACGTTAAGTAGAGTGGAAAATTACTTAAGTGACGGTATCTAACCAGAAAGGGACGGCTAACTACGTG ->Cluster_9 -TGCAAGTCGAACGCACTGTGGTTCAACTGATTTGAAGAGCTTGCTCTGATATGACGATGAACATTGCAGTGAGTGGCGAACGGGTGAGTAACACGTGGGAAACCTACCTCTTAGCGGGGGATAACATCTGGAAACAGATGCTAATACCGCATAACACTAGCAACCGCATGGTTGCTACTTGAAAGATGGTTCTGCTATCACTAAGAGATGGTCCCGCGGCGCATTAGTTAGTTGGTGAGGTAATGGCTCACCAAGACGATGATGCGTAGCCGAGTTGAGAGACTGATCGGCCACAATGGGACTGAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGTGTGATGAAGGGTTTCGGCTCGTAAAACACTGTTGTAAGAGAAGAATAGCATTGAGAGTAACTGCTCAGTGTCTGACGGTATCTTACCAGAAAGGAACGGCTAAATACGTG ->Cluster_10 -GATGAACGCTAGCGGCAGGCTTAACACATGCAAGTCGAGGGGTATAGTTCTTCGGAACTAGAGACCGGCGCACGGGTGCGTAACGCGTATGCAATCTACCTTTTACAGAGGGATAGCCCAGAGAAATTTGGATTAATACCTCATAGCATTGCAGAATGGCATCATTCAGCAATTAAAGTCACAACGGTAAAAGATGAGCATGCGTCCCATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCTACGATGGGTAGGGGTCCTGAGAGGGAGATCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGCAGGATGACGGTCCTATGGATTGTAAAACTGCTTTT |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/1683619172.2099853_50503_tmp_place_seqs.log --- a/test-data/1683619172.2099853_50503_tmp_place_seqs.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,21 +0,0 @@ -hmmalign --trim --dna --mapali /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /tmp/tmpyh8h10gg/query_align.stockholm /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm 1683619172.2099853_50503_cleaned.fasta - -Raw input sequences ranged in length from 408 to 520 - -run_sepp.py --tree /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpyh8h10gg/sepp_out -seed 297834 --alignment /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpyh8h10gg/study_seqs_filtered.fasta - -Error running this command: -run_sepp.py --tree /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpyh8h10gg/sepp_out -seed 297834 --alignment /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpyh8h10gg/study_seqs_filtered.fasta - -Standard error of the above failed command: -Traceback (most recent call last): - File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/bin/run_sepp.py", line 3, in <module> - from sepp.exhaustive import ExhaustiveAlgorithm - File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/exhaustive.py", line 6, in <module> - from sepp.algorithm import AbstractAlgorithm - File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/algorithm.py", line 11, in <module> - from sepp.tree import PhylogeneticTree - File "/home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/lib/python3.6/site-packages/sepp/tree.py", line 25, in <module> - from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ -ImportError: cannot import name '_convert_node_to_root_polytomy' - |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/1683625674.1083791_56412_genes_abundances_formatted.tsv --- a/test-data/1683625674.1083791_56412_genes_abundances_formatted.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
b'@@ -1,1108 +0,0 @@\n-function\tSC1703-104_TTGCCC-B6TML_L001_R\tSC1703-105_CAGTCT-B6TML_L001_R\tSC1703-106_TTAAAT-B6TML_L001_R\tSC1703-107_AATTGC-B6TML_L001_R\tSC1703-108_ACTCGA-B6TML_L001_R\tSC1703-109_GTTACC-B6TML_L001_R\tSC1703-110_CAGATG-B6TML_L001_R\tSC1703-125_TCGCGC-B6TML_L001_R\tSC1703-126_TAACTT-B6TML_L001_R\tSC1703-127_CTGTAA-B6TML_L001_R\tSC1703-128_CCATTG-B6TML_L001_R\tSC1703-129_TAGGCT-B6TML_L001_R\tSC1703-130_TTCTTG-B6TML_L001_R\tSC1703-131_CCGACC-B6TML_L001_R\tSC1703-132_TTAGCT-B6TML_L001_R\tSC1703-133_CAGAGC-B6TML_L001_R\tSC1703-134_AATATG-B6TML_L001_R\tSC1703-135_TGAGCA-B6TML_L001_R\tSC1703-136_AATCAC-B6TML_L001_R\tSC1703-137_GGTAGC-B6TML_L001_R\tSC1703-138_CTCTCG-B6TML_L001_R\tSC1703-145_AGCGAC-B6TML_L001_R\tSC1703-146_GCCAAG-B6TML_L001_R\tSC1703-147_AGGTTC-B6TML_L001_R\tSC1703-148_TTTTTC-B6TML_L001_R\tSC1703-149_GTCGTG-B6TML_L001_R\tSC1703-150_GCTATC-B6TML_L001_R\tSC1703-151_TATGCG-B6TML_L001_R\tSC1703-41_TCGTTC-B6TML_L001_R\tSC1703-42_GCGATG-B6TML_L001_R\tSC1703-43_ATATAA-B6TML_L001_R\tSC1703-44_ATACTG-B6TML_L001_R\tSC1703-45_GGAGAG-B6TML_L001_R\tSC1703-46_ACGAGA-B6TML_L001_R\tSC1703-47_ATTACA-B6TML_L001_R\tSC1703-48_TGATTT-B6TML_L001_R\tSC1703-49_GGGGTG-B6TML_L001_R\tSC1703-50_ACAAAA-B6TML_L001_R\tSC1703-51_CTCCAG-B6TML_L001_R\tSC1703-52_GGTGTT-B6TML_L001_R\tSC1703-53_CGGGAG-B6TML_L001_R\tSC1703-54_TGGTAG-B6TML_L001_R\tSC1703-62_TGCGGG-B6TML_L001_R\tSC1703-63_TCTATG-B6TML_L001_R\tSC1703-64_GGACGG-B6TML_L001_R\tSC1703-65_AGAGGG-B6TML_L001_R\tSC1703-66_ATGAAC-B6TML_L001_R\tSC1703-67_TACCTG-B6TML_L001_R\tSC1703-68_CTAGAG-B6TML_L001_R\tSC1703-83_CTTGCA-B6TML_L001_R\tSC1703-84_CATGTT-B6TML_L001_R\tSC1703-85_TGGATT-B6TML_L001_R\tSC1703-86_AACGCA-B6TML_L001_R\tSC1703-87_TTCGAG-B6TML_L001_R\tSC1703-88_AAGCTA-B6TML_L001_R\tSC1703-89_AGTTTG-B6TML_L001_R\tSC1703-90_TCCCCA-B6TML_L001_R\tSC1703-91_AACTAG-B6TML_L001_R\tSC1703-92_GTTCGC-B6TML_L001_R\tSC1703-93_TGCCTT-B6TML_L001_R\tSC1703-94_ATAAGA-B6TML_L001_R\tSC1703-95_CACACT-B6TML_L001_R\tSC1703-96_ACAGTT-B6TML_L001_R\n-EC:1.1.1.1\t11566.34\t23536.0\t22817.34\t31136.66\t15901.0\t8184.34\t15871.34\t8008.34\t21032.66\t39229.0\t32995.0\t35887.66\t17682.34\t36119.34\t26352.66\t18487.66\t14950.0\t28138.34\t17895.66\t19944.34\t31250.66\t10575.34\t10181.34\t10813.66\t14690.34\t8468.66\t14335.66\t7767.0\t13431.66\t7180.34\t15309.66\t16261.66\t12751.0\t11576.0\t20053.34\t20050.0\t15420.34\t12877.66\t19375.66\t22396.0\t15726.66\t22287.0\t19666.66\t21662.34\t13317.0\t21680.0\t30628.0\t16063.34\t22263.66\t13229.34\t14780.34\t21428.34\t19434.66\t24648.0\t12879.66\t16019.0\t23014.34\t34206.66\t36327.0\t32828.66\t25381.66\t31395.66\t23572.66\n-EC:1.1.1.100\t23686.67\t42044.0\t40635.67\t56035.33\t28377.0\t15681.67\t29555.67\t23492.67\t57202.33\t86339.0\t81825.0\t94005.33\t36279.67\t86889.67\t61062.33\t43328.33\t45341.0\t85663.67\t64190.33\t50519.67\t74343.33\t25978.67\t19038.67\t19813.33\t29918.67\t15076.33\t25533.33\t16220.0\t36736.33\t14913.67\t39478.33\t34167.33\t36721.0\t14972.0\t61435.67\t66863.0\t48295.67\t26697.33\t64452.33\t74769.0\t52517.33\t78847.0\t35290.33\t39231.67\t27046.0\t36638.0\t60910.0\t27032.67\t40679.33\t33098.67\t34174.67\t76333.67\t34090.33\t74998.0\t38132.33\t41871.0\t86148.67\t105473.33\t109284.0\t98252.33\t76729.33\t101539.33\t74591.33\n-EC:1.1.1.103\t365.66999999999996\t1758.0\t2244.67\t2728.33\t1320.0\t530.67\t1323.67\t3111.67\t8110.33\t1128.0\t8049.0\t10893.33\t530.67\t7177.67\t6433.33\t4150.33\t3801.0\t3445.67\t7990.33\t4822.67\t6503.33\t328.66999999999996\t1495.67\t251.32999999999998\t533.6700000000001\t386.33\t560.3299999999999\t127.0\t6481.33\t1764.67\t6107.33\t4176.33\t7477.0\t5151.0\t11258.67\t8114.0\t5743.67\t4673.33\t7871.33\t6544.0\t4010.33\t5379.0\t694.3299999999999\t2645.67\t1111.0\t770.0\t1491.0\t1649.67\t839.33\t5247.67\t5273.67\t12700.67\t2326.33\t14896.0\t5965.33\t6284.0\t8740.67\t14261.33\t6323.0\t16592.33\t11098.33\t12453.33\t9603.33\n-EC:1.1.1.108\t350.0\t336.0\t1010.0\t520.0\t280.0\t676.0\t632.0\t2110.0\t982.0\t9000.0\t2012.0\t896.0\t3294.0\t2382.0\t646.0\t1364.0\t1542.0\t1020.0\t1678.0\t2464.0\t1416.0\t22.0\t396.0\t52.0\t448.0\t64.0\t100.0\t22.0\t1118.0\t526.0\t562.0\t5294.0\t142.0\t1052.0\t1750.0\t2044.0\t1224.0\t206.0\t538.0\t742.0\t764.0\t542.0\t716.0\t1738.0\t592.0\t696.0\t1172.0\t736.0\t1254.0\t2768.0\t3600.0\t1226.0\t6276.0\t2998.0\t19'..b'0000002\t12767.99\t20010.010000000002\t9893.99\t20105.989999999998\t13193.0\t28942.989999999998\t11903.01\t32763.989999999998\t29710.989999999998\t27427.0\t19192.0\t46246.01\t67305.0\t35829.01\t31605.989999999998\t56382.990000000005\t74728.0\t49632.990000000005\t59538.0\t31783.989999999998\t36392.01\t28064.0\t30045.0\t56888.0\t26349.010000000002\t37149.99\t26415.010000000002\t29572.010000000002\t55220.01\t39441.99\t57808.0\t29285.989999999998\t34998.0\t97755.01000000001\t87529.98999999999\t73205.0\t85625.98999999999\t57513.99\t70984.98999999999\t61546.99\n-EC:6.5.1.1\t1148.0\t1468.0\t1044.0\t1396.0\t552.0\t612.0\t1846.0\t13.0\t13.0\t15.0\t35.0\t9.0\t24.0\t21.0\t2666.0\t728.0\t4407.0\t3321.0\t9514.0\t1597.0\t2373.0\t969.0\t372.0\t97.0\t697.0\t42.0\t836.0\t399.0\t1.0\t2.0\t6.0\t8.0\t6.0\t7.0\t4.0\t5184.0\t1406.0\t2379.0\t1471.0\t4165.0\t2616.0\t473.0\t1876.0\t1757.0\t3013.0\t1270.0\t2225.0\t1771.0\t3610.0\t41.0\t20.0\t32.0\t76.0\t34.0\t22.0\t11.0\t15266.0\t4545.0\t2580.0\t2981.0\t1403.0\t638.0\t3822.0\n-EC:6.5.1.2\t8751.34\t15264.0\t15146.34\t21089.66\t10802.0\t5733.34\t12410.34\t7098.34\t20732.66\t37536.0\t32708.0\t36358.66\t16192.34\t36335.34\t26674.66\t16116.66\t17938.0\t30332.34\t26177.66\t18519.34\t27455.66\t9672.34\t7485.34\t6763.66\t10845.34\t5560.66\t9577.66\t5737.0\t14144.66\t7155.34\t18968.66\t14757.66\t12353.0\t10722.0\t20850.34\t24333.0\t18266.34\t15306.66\t21033.66\t27182.0\t19404.66\t26779.0\t13610.66\t15454.34\t11847.0\t13377.0\t22921.0\t11928.34\t16614.66\t12398.34\t13183.34\t24728.34\t16000.66\t24020.0\t13390.66\t13055.0\t35987.34\t36372.66\t39220.0\t34196.66\t25445.66\t34642.66\t26649.66\n-EC:6.5.1.3\t132.67\t453.0\t906.67\t1233.33\t722.0\t182.67\t928.67\t237.67\t950.33\t1103.0\t1135.0\t958.33\t515.67\t1343.67\t3260.33\t1374.33\t662.0\t396.67\t632.33\t1306.67\t1684.33\t239.67\t727.67\t93.33\t328.67\t323.33\t356.33\t55.0\t1850.33\t1268.67\t3304.33\t2625.33\t1246.0\t3807.0\t1892.67\t771.0\t1328.67\t3151.33\t536.33\t721.0\t546.33\t252.0\t469.33\t1188.67\t646.0\t345.0\t913.0\t1204.67\t568.33\t1654.67\t1865.67\t1165.67\t2281.33\t2042.0\t1188.33\t1036.0\t298.67\t1628.33\t1064.0\t2668.33\t1511.33\t1775.33\t1288.33\n-EC:6.5.1.4\t132.67\t453.0\t906.67\t1233.33\t722.0\t182.67\t928.67\t237.67\t950.33\t1103.0\t1135.0\t958.33\t515.67\t1343.67\t3260.33\t1374.33\t662.0\t396.67\t632.33\t1306.67\t1684.33\t239.67\t727.67\t93.33\t328.67\t323.33\t356.33\t55.0\t1850.33\t1268.67\t3304.33\t2625.33\t1246.0\t3807.0\t1892.67\t771.0\t1328.67\t3151.33\t536.33\t721.0\t546.33\t252.0\t469.33\t1188.67\t646.0\t345.0\t913.0\t1204.67\t568.33\t1654.67\t1865.67\t1165.67\t2281.33\t2042.0\t1188.33\t1036.0\t298.67\t1628.33\t1064.0\t2668.33\t1511.33\t1775.33\t1288.33\n-EC:6.5.1.6\t1148.0\t1468.0\t1044.0\t1396.0\t552.0\t612.0\t1846.0\t13.0\t13.0\t15.0\t35.0\t9.0\t24.0\t21.0\t2666.0\t728.0\t4407.0\t3321.0\t9514.0\t1597.0\t2373.0\t969.0\t372.0\t97.0\t697.0\t42.0\t836.0\t399.0\t1.0\t2.0\t6.0\t8.0\t6.0\t7.0\t4.0\t5184.0\t1406.0\t2379.0\t1471.0\t4165.0\t2616.0\t473.0\t1876.0\t1757.0\t3013.0\t1270.0\t2225.0\t1771.0\t3610.0\t41.0\t20.0\t32.0\t76.0\t34.0\t22.0\t11.0\t15266.0\t4545.0\t2580.0\t2981.0\t1403.0\t638.0\t3822.0\n-EC:6.5.1.7\t1148.0\t1468.0\t1044.0\t1396.0\t552.0\t612.0\t1846.0\t13.0\t13.0\t15.0\t35.0\t9.0\t24.0\t21.0\t2666.0\t728.0\t4407.0\t3321.0\t9514.0\t1597.0\t2373.0\t969.0\t372.0\t97.0\t697.0\t42.0\t836.0\t399.0\t1.0\t2.0\t6.0\t8.0\t6.0\t7.0\t4.0\t5184.0\t1406.0\t2379.0\t1471.0\t4165.0\t2616.0\t473.0\t1876.0\t1757.0\t3013.0\t1270.0\t2225.0\t1771.0\t3610.0\t41.0\t20.0\t32.0\t76.0\t34.0\t22.0\t11.0\t15266.0\t4545.0\t2580.0\t2981.0\t1403.0\t638.0\t3822.0\n-EC:6.6.1.1\t350.0\t336.0\t1010.0\t520.0\t280.0\t676.0\t632.0\t2110.0\t982.0\t9000.0\t2012.0\t896.0\t3294.0\t2382.0\t646.0\t1364.0\t1542.0\t1020.0\t1678.0\t2464.0\t1416.0\t22.0\t396.0\t52.0\t448.0\t64.0\t100.0\t22.0\t1118.0\t526.0\t562.0\t5294.0\t142.0\t1052.0\t1750.0\t2044.0\t1224.0\t206.0\t538.0\t742.0\t764.0\t542.0\t716.0\t1738.0\t592.0\t696.0\t1172.0\t736.0\t1254.0\t2768.0\t3600.0\t1226.0\t6276.0\t2998.0\t1956.0\t6350.0\t3722.0\t3902.0\t3776.0\t3310.0\t2710.0\t1822.0\t2832.0\n-EC:6.6.1.2\t175.0\t168.0\t505.0\t260.0\t140.0\t338.0\t316.0\t1055.0\t491.0\t4500.0\t1006.0\t448.0\t1647.0\t1191.0\t323.0\t682.0\t771.0\t510.0\t839.0\t1232.0\t708.0\t11.0\t198.0\t26.0\t224.0\t32.0\t50.0\t11.0\t559.0\t263.0\t281.0\t2647.0\t71.0\t526.0\t875.0\t1022.0\t612.0\t103.0\t269.0\t371.0\t382.0\t271.0\t358.0\t869.0\t296.0\t348.0\t586.0\t368.0\t627.0\t1384.0\t1800.0\t613.0\t3138.0\t1499.0\t978.0\t3175.0\t1861.0\t1951.0\t1888.0\t1655.0\t1355.0\t911.0\t1416.0\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/EC_copynumbers_predicted.tsv --- a/test-data/EC_copynumbers_predicted.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
b'@@ -1,11 +0,0 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b |
diff -r b2967b704d6b -r f479218f3736 test-data/affi-filterd.log --- a/test-data/affi-filterd.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,3322 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpmzhyhv__/galaxy-dev\n-Clonage dans \'/tmp/tmpmzhyhv__/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'acted.multihit.tsv" ] ; then cp "/tmp/tmptwvvejsv/job_working_directory/000/6/working/impacted.multihit.tsv" "/tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_58015c1b-4f2a-4004-aa4e-aafd157dff6a.dat" ; fi; \n-if [ -f "/tmp/tmptwvvejsv/job_working_directory/000/6/working/report.html" ] ; then cp "/tmp/tmptwvvejsv/job_working_directory/000/6/working/report.html" "/tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_6919cff3-b2ec-4755-8bd6-36005c576a20.dat" ; fi; cd \'/tmp/tmptwvvejsv/job_working_directory/000/6\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-26 11:36:48,965 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] (6) executing job script: /tmp/tmptwvvejsv/job_working_directory/000/6/galaxy_6.sh\n-galaxy.web_stack DEBUG 2023-04-26 11:36:48,977 [pN:main.1,p:213974,tN:Thread-9] server_name set to: main.1\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-26 11:36:54,124 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 213974\n-galaxy.jobs.runners.local DEBUG 2023-04-26 11:36:54,125 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmptwvvejsv/job_working_directory/000/6/galaxy_6.sh\n-\n-galaxy.jobs DEBUG 2023-04-26 11:36:55,753 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_eb946f9d-6a69-44d9-9e07-5cdfb2e8f303.dat to /tmp/tmptwvvejsv/files/e/b/9/dataset_eb946f9d-6a69-44d9-9e07-5cdfb2e8f303.dat\n-galaxy.jobs DEBUG 2023-04-26 11:36:55,753 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_203c65c0-5cdd-41b8-acf5-30686db81fac.dat to /tmp/tmptwvvejsv/files/2/0/3/dataset_203c65c0-5cdd-41b8-acf5-30686db81fac.dat\n-galaxy.jobs DEBUG 2023-04-26 11:36:55,754 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_f4c6a30a-8a47-406c-bab8-1af4180c5d8f.dat to /tmp/tmptwvvejsv/files/f/4/c/dataset_f4c6a30a-8a47-406c-bab8-1af4180c5d8f.dat\n-galaxy.jobs DEBUG 2023-04-26 11:36:55,754 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_58015c1b-4f2a-4004-aa4e-aafd157dff6a.dat to /tmp/tmptwvvejsv/files/5/8/0/dataset_58015c1b-4f2a-4004-aa4e-aafd157dff6a.dat\n-galaxy.jobs DEBUG 2023-04-26 11:36:55,754 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmptwvvejsv/job_working_directory/000/6/outputs/galaxy_dataset_6919cff3-b2ec-4755-8bd6-36005c576a20.dat to /tmp/tmptwvvejsv/files/6/9/1/dataset_6919cff3-b2ec-4755-8bd6-36005c576a20.dat\n-galaxy.model.metadata DEBUG 2023-04-26 11:36:55,789 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 9\n-galaxy.model.metadata DEBUG 2023-04-26 11:36:55,805 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 10\n-galaxy.model.metadata DEBUG 2023-04-26 11:36:55,821 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 11\n-galaxy.model.metadata DEBUG 2023-04-26 11:36:55,855 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 12\n-galaxy.model.metadata DEBUG 2023-04-26 11:36:55,889 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 13\n-\n-galaxy.jobs DEBUG 2023-04-26 11:36:56,762 [pN:main.1,p:213088,tN:LocalRunner.work_thread-2] job_wrapper.finish for job 6 executed (1014.947 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 2 test(s) executed passed.\n-FROGS_affiliation_filters (Test #1): passed\n-FROGS_affiliation_filters (Test #2): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/affi-stats.log --- a/test-data/affi-stats.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1853 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpvm6ztn8s/galaxy-dev\n-Clonage dans \'/tmp/tmpvm6ztn8s/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'read-0] Job wrapper for Job [2] prepared (109.492 ms)\n-galaxy.tool_util.deps DEBUG 2023-04-26 11:49:32,617 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] Using dependency frogs version 4.1.0 of type conda\n-galaxy.tool_util.deps DEBUG 2023-04-26 11:49:32,617 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] Using dependency frogs version 4.1.0 of type conda\n-galaxy.jobs.command_factory INFO 2023-04-26 11:49:32,635 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] Built script [/tmp/tmpvm6ztn8s/job_working_directory/000/2/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; affiliation_stats.py --input-biom \'/tmp/tmpvm6ztn8s/files/e/9/2/dataset_e921953b-5d8b-4280-86cf-3a17cbd1b979.dat\' --output-file \'/tmp/tmpvm6ztn8s/job_working_directory/000/2/outputs/galaxy_dataset_f6c8fb33-f2bb-4d6a-9fb6-5e68a72509ac.dat\' --taxonomic-ranks Domain Phylum Class Order Family Genus Species --rarefaction-ranks Family Genus Species --multiple-tag \'blast_affiliations\' --tax-consensus-tag \'blast_taxonomy\' --identity-tag \'perc_identity\' --coverage-tag \'perc_query_coverage\']\n-galaxy.jobs.runners DEBUG 2023-04-26 11:49:32,725 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpvm6ztn8s/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpvm6ztn8s/job_working_directory/000/2/galaxy_2.ec; \n-if [ -f "/tmp/tmpvm6ztn8s/job_working_directory/000/2/working/summary.html" ] ; then cp "/tmp/tmpvm6ztn8s/job_working_directory/000/2/working/summary.html" "/tmp/tmpvm6ztn8s/job_working_directory/000/2/outputs/galaxy_dataset_f6c8fb33-f2bb-4d6a-9fb6-5e68a72509ac.dat" ; fi; cd \'/tmp/tmpvm6ztn8s/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-26 11:49:32,749 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] (2) executing job script: /tmp/tmpvm6ztn8s/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-26 11:49:39,274 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 215091\n-galaxy.jobs.runners.local DEBUG 2023-04-26 11:49:39,274 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpvm6ztn8s/job_working_directory/000/2/galaxy_2.sh\n-galaxy.jobs DEBUG 2023-04-26 11:49:39,326 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpvm6ztn8s/job_working_directory/000/2/outputs/galaxy_dataset_f6c8fb33-f2bb-4d6a-9fb6-5e68a72509ac.dat to /tmp/tmpvm6ztn8s/files/f/6/c/dataset_f6c8fb33-f2bb-4d6a-9fb6-5e68a72509ac.dat\n-galaxy.model.metadata DEBUG 2023-04-26 11:49:39,407 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 2\n-galaxy.jobs DEBUG 2023-04-26 11:49:39,540 [pN:main.1,p:215036,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 2 executed (230.314 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_affiliation_stats (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/affiliation_abundance.biom --- a/test-data/affiliation_abundance.biom Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1 +0,0 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2023-04-14T07:56:49", "rows": [{"id": "Cluster_1", "metadata": {"comment": [], "seed_id": "01_54", "blast_affiliations": [{"subject": "JF747094_SH197643.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Chaetothyriales", "f__Herpotrichiellaceae", "g__Exophiala", "s__Exophiala_equina"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_2", "metadata": {"comment": [], "seed_id": "01_92546", "blast_affiliations": [{"subject": "DQ898183_SH216206.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "evalue": "2.25e-132", "aln_length": 249, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Pezizomycetes", "o__Pezizales", "f__Tuberaceae", "g__Tuber", "s__Tuber_latisporum"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_3", "metadata": {"comment": [], "seed_id": "01_59", "blast_affiliations": [{"subject": "JN711441_SH022548.07FU_refs_singleton", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "evalue": "8.06e-132", "aln_length": 248, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Eurotiomycetes", "o__Eurotiales", "f__Elaphomycetaceae", "g__Elaphomyces", "s__Elaphomyces_compleximurus"], "rdp_bootstrap": [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]}}, {"id": "Cluster_4", "metadata": {"comment": [], "seed_id": "01_81", "blast_affiliations": [{"subject": "AF456924_SH097201.07FU_refs", "taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "evalue": "4.90e-134", "aln_length": 252, "perc_identity": 100.0, "perc_query_coverage": 100.0}], "blast_taxonomy": ["k__Fungi", "p__Ascomycota", "c__Sordariomycetes", "o__Hypocreales", "f__Hypocreaceae", "g__Trichoderma", "s__Trichoderma_aggressivum"], "rdp_taxonomy": 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diff -r b2967b704d6b -r f479218f3736 test-data/all_tool_test_output.html --- a/test-data/all_tool_test_output.html Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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diff -r b2967b704d6b -r f479218f3736 test-data/biom_to_tsv.log --- a/test-data/biom_to_tsv.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1999 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp_alx6hte/galaxy-dev\n-Clonage dans \'/tmp/tmp_alx6hte/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b' $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; biom_to_tsv.py --input-biom \'/tmp/tmp_alx6hte/files/0/b/a/dataset_0baedaa9-8f4a-45da-8053-1ec4e7a1a1e0.dat\' --input-fasta \'/tmp/tmp_alx6hte/files/0/2/0/dataset_020940d9-f049-4320-a3d7-e944a3ccbd81.dat\' --output-tsv \'/tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_23178c6b-2652-4e59-bde8-755de1e116d4.dat\' --output-multi-affi \'/tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_172a24d1-ad2e-46fe-9fb0-afdcf88c2ff2.dat\']\n-\n-galaxy.jobs.runners DEBUG 2023-04-26 10:42:03,389 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] (3) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmp_alx6hte/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp_alx6hte/job_working_directory/000/3/galaxy_3.ec; \n-if [ -f "/tmp/tmp_alx6hte/job_working_directory/000/3/working/abundance.tsv" ] ; then cp "/tmp/tmp_alx6hte/job_working_directory/000/3/working/abundance.tsv" "/tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_23178c6b-2652-4e59-bde8-755de1e116d4.dat" ; fi; \n-if [ -f "/tmp/tmp_alx6hte/job_working_directory/000/3/working/multi_hits.tsv" ] ; then cp "/tmp/tmp_alx6hte/job_working_directory/000/3/working/multi_hits.tsv" "/tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_172a24d1-ad2e-46fe-9fb0-afdcf88c2ff2.dat" ; fi; cd \'/tmp/tmp_alx6hte/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-26 10:42:03,419 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] (3) executing job script: /tmp/tmp_alx6hte/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-26 10:42:11,015 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 207856\n-galaxy.jobs.runners.local DEBUG 2023-04-26 10:42:11,015 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmp_alx6hte/job_working_directory/000/3/galaxy_3.sh\n-galaxy.jobs DEBUG 2023-04-26 10:42:11,045 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_23178c6b-2652-4e59-bde8-755de1e116d4.dat to /tmp/tmp_alx6hte/files/2/3/1/dataset_23178c6b-2652-4e59-bde8-755de1e116d4.dat\n-galaxy.jobs DEBUG 2023-04-26 10:42:11,046 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp_alx6hte/job_working_directory/000/3/outputs/galaxy_dataset_172a24d1-ad2e-46fe-9fb0-afdcf88c2ff2.dat to /tmp/tmp_alx6hte/files/1/7/2/dataset_172a24d1-ad2e-46fe-9fb0-afdcf88c2ff2.dat\n-galaxy.model.metadata DEBUG 2023-04-26 10:42:11,091 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.model.metadata DEBUG 2023-04-26 10:42:11,105 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 4\n-galaxy.jobs DEBUG 2023-04-26 10:42:11,187 [pN:main.1,p:207742,tN:LocalRunner.work_thread-3] job_wrapper.finish for job 3 executed (148.539 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_biom_to_tsv (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/chaillou.tsv --- a/test-data/chaillou.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
b'@@ -1,509 +0,0 @@\n-#taxonomy\tobservation_name\tobservation_sum\tDLT0.LOT08\tDLT0.LOT05\tDLT0.LOT03\tDLT0.LOT07\tDLT0.LOT06\tDLT0.LOT01\tDLT0.LOT04\tDLT0.LOT10\tMVT0.LOT05\tMVT0.LOT01\tMVT0.LOT06\tMVT0.LOT07\tMVT0.LOT03\tMVT0.LOT09\tMVT0.LOT08\tMVT0.LOT10\tBHT0.LOT01\tBHT0.LOT07\tBHT0.LOT06\tBHT0.LOT03\tBHT0.LOT10\tBHT0.LOT05\tBHT0.LOT04\tBHT0.LOT08\tVHT0.LOT02\tVHT0.LOT10\tVHT0.LOT03\tVHT0.LOT01\tVHT0.LOT08\tVHT0.LOT06\tVHT0.LOT07\tVHT0.LOT04\tSFT0.LOT08\tSFT0.LOT07\tSFT0.LOT06\tSFT0.LOT03\tSFT0.LOT02\tSFT0.LOT05\tSFT0.LOT04\tSFT0.LOT01\tFST0.LOT07\tFST0.LOT08\tFST0.LOT05\tFST0.LOT06\tFST0.LOT01\tFST0.LOT03\tFST0.LOT10\tFST0.LOT02\tFCT0.LOT06\tFCT0.LOT10\tFCT0.LOT05\tFCT0.LOT03\tFCT0.LOT08\tFCT0.LOT02\tFCT0.LOT07\tFCT0.LOT01\tCDT0.LOT10\tCDT0.LOT08\tCDT0.LOT05\tCDT0.LOT04\tCDT0.LOT06\tCDT0.LOT09\tCDT0.LOT07\tCDT0.LOT02\n-k__Bacteria;p__Tenericutes;c__Mollicutes;o__Mycoplasmatales;f__Mycoplasmataceae;g__Candidatus Lumbricincola;s__NA\totu_01778\t200\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t98\t23\t10\t16\t19\t4\t30\t0\t0\t0\t0\t0\t0\t0\t0\n-k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__NA\totu_01838\t444\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9\t4\t0\t0\t4\t3\t3\t0\t5\t9\t2\t371\t4\t19\t11\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Dyella;s__Ginsengisoli\totu_01386\t453\t4\t0\t0\t7\t7\t9\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t3\t3\t2\t25\t2\t10\t6\t5\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t46\t21\t27\t108\t73\t33\t49\t0\t0\t0\t0\t0\t0\t0\t0\n-k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Planococcaceae;g__Incertae Sedis;s__NA\totu_01835\t197\t13\t118\t6\t0\t0\t8\t2\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t2\t8\t4\t4\t5\t0\t3\t5\n-k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__NA\totu_01837\t538\t9\t9\t16\t0\t7\t10\t2\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t9\t6\t0\t0\t2\t7\t6\t3\t4\t0\t0\t3\t3\t0\t13\t0\t2\t52\t19\t8\t4\t12\t41\t32\t64\t5\t5\t64\t112\n-k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae;g__Weissella;s__NA\totu_01832\t152\t0\t0\t0\t91\t0\t0\t0\t36\t0\t0\t0\t0\t6\t0\t0\t0\t4\t0\t0\t0\t0\t2\t0\t0\t0\t9\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces;s__NA\totu_01833\t225\t0\t0\t0\t0\t3\t26\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t4\t61\t8\t3\t6\t6\t3\t59\t0\t0\t10\t0\t3\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t17\t0\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Micrococcales;f__Brevibacteriaceae;g__Brevibacterium;s__Marinum\totu_00156\t229\t0\t0\t0\t0\t0\t0\t0\t3\t24\t0\t25\t20\t13\t32\t20\t7\t0\t8\t0\t0\t0\t0\t3\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t11\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t7\t0\t0\t0\t0\t15\t0\t0\t0\t3\t23\t8\n-k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales;f__Neisseriaceae;g__Neisseria;s__Perflava\totu_01719\t203\t2\t3\t4\t17\t29\t16\t23\t15\t0\t0\t10\t8\t0\t0\t0\t0\t6\t3\t4\t10\t0\t2\t0\t0\t20\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t28\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia;s__Tabacinasalis\totu_00015\t405\t0\t1\t0\t0\t4\t0\t2\t0\t4\t0\t0\t0\t0\t0\t0\t0\t15\t9\t25\t17\t9\t5\t103\t18\t14\t8\t25\t28\t44\t19\t19\t26\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\n-k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Sakei\totu_00769\t53573\t15\t9\t126\t191\t115\t208\t37\t150\t4116\t4069\t937\t1516\t395\t1818\t6200\t8784\t461\t91\t106\t270\t102\t279\t166\t156\t114\t21\t175\t90\t46\t68\t73\t63\t141\t3563\t1494\t3678\t5081\t13\t965\t138\t65\t2256\t2171\t1996\t23\t71\t30\t31\t2\t202\t49\t30\t144\t83\t123\t133\t2\t2\t38\t60\t6\t3\t4\t9\n-k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Brevis\totu_00768\t438\t0\t0\t0\t0\t4\t0\t0\t7\t0\t0\t15\t0\t13\t24\t0\t0\t4\t25\t225\t20\t3\t3\t74\t19\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__'..b'eria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Family XI Incertae Sedis;g__Gemella;s__Haemolysans\totu_01748\t187\t5\t5\t6\t6\t9\t13\t3\t15\t0\t0\t0\t0\t8\t0\t0\t0\t0\t0\t0\t0\t0\t4\t5\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t75\t6\t0\t0\t3\t7\t5\t5\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Propionibacteriales;f__Propionibacteriaceae;g__Luteococcus;s__Japonicus\totu_01747\t2123\t25\t5\t173\t66\t25\t25\t2\t19\t4\t0\t10\t0\t6\t0\t6\t0\t8\t930\t63\t35\t83\t64\t312\t147\t3\t2\t10\t4\t0\t5\t3\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t7\t0\t13\t0\t0\t0\t5\t2\t10\t0\t4\t13\t0\t0\t14\t8\t3\t3\t0\t0\n-k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Rhodocyclales;f__Rhodocyclaceae;g__Methyloversatilis;s__Universalis\totu_01744\t111\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t31\t3\t0\t0\t0\t5\t2\t0\t6\t0\t0\t0\t0\t5\t5\t0\t0\t3\t2\t4\t0\t0\t4\t0\t0\t15\t3\t2\t0\t3\t13\n-k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Family XI Incertae Sedis;g__Tissierella;s__NA\totu_01740\t506\t2\t7\t8\t0\t20\t9\t2\t0\t40\t9\t80\t85\t19\t80\t15\t49\t0\t5\t4\t0\t0\t7\t10\t16\t4\t2\t4\t5\t0\t2\t3\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\n-k__Bacteria;p__Candidate division TM7;c__NA;o__NA;f__NA;g__NA;s__NA\totu_01741\t250\t0\t0\t0\t0\t0\t0\t0\t0\t4\t6\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t7\t0\t3\t0\t12\t10\t2\t195\t0\t3\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Terrigena\totu_00695\t602\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t17\t0\t0\t0\t0\t0\t0\t7\t0\t9\t6\t0\t0\t0\t13\t116\t180\t141\t8\t4\t10\t16\t0\t0\t4\t3\t5\t16\t7\t4\t2\t0\t11\t14\t0\t3\t3\t0\n-k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Hibernum\totu_00694\t416\t3\t0\t7\t0\t44\t26\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t83\t26\t0\t4\t29\t24\t92\t16\t0\t0\t41\t11\t0\t2\t0\t0\n-k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Cheniae\totu_00693\t430\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t3\t1\t0\t2\t0\t6\t1\t0\t0\t7\t69\t166\t97\t7\t10\t22\t11\t0\t0\t0\t0\t4\t8\t0\t3\t0\t0\t3\t5\t0\t0\t0\t0\n-k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Wautersiella;s__Falsenii\totu_00519\t2807\t3\t14\t0\t9\t8\t0\t26\t16\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t37\t7\t4\t0\t0\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t570\t92\t29\t5\t4\t1908\t66\n-k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Frigidarium\totu_00690\t3053\t0\t0\t2\t0\t7\t7\t0\t0\t0\t0\t0\t0\t0\t16\t0\t0\t11\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t109\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t7\t9\t3\t4\t3\t4\t5\t3\t98\t564\t18\t206\t43\t42\t459\t1319\t0\t3\t65\t36\t0\t0\t3\t3\n-k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Arsenicoxydans\totu_01184\t87\t0\t0\t0\t0\t4\t2\t0\t0\t10\t15\t20\t0\t19\t0\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t0\n-k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Empedobacter;s__NA\totu_00516\t378\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t2\t8\t3\t4\t2\t306\t51\n-k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Syringae\totu_01187\t1532\t3\t14\t10\t110\t95\t30\t479\t12\t6\t6\t65\t8\t68\t0\t0\t0\t0\t0\t3\t16\t3\t0\t3\t3\t3\t16\t4\t3\t8\t187\t3\t3\t3\t7\t2\t9\t0\t0\t5\t0\t7\t36\t41\t37\t12\t7\t15\t13\t95\t6\t0\t7\t7\t7\t36\t11\t0\t0\t3\t3\t0\t2\t0\t0\n-k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Cedrina\totu_01182\t442\t2\t1\t5\t11\t8\t18\t73\t11\t0\t15\t10\t0\t29\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t11\t3\t12\t3\t0\t0\t3\t125\t11\t2\t4\t4\t0\t42\t7\t3\t0\t0\t8\t0\t3\t4\t4\n-k__Bacteria;p__Bacteroidetes;c__Flavobacteria;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Suncheonense\totu_00698\t333\t0\t0\t0\t3\t0\t3\t0\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t2\t9\t6\t1\t0\t2\t7\t33\t0\t20\t0\t4\t3\t3\t2\t4\t0\t2\t8\t8\t0\t3\t0\t29\t101\t41\t3\t2\t7\t20\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/cluster_filters.log --- a/test-data/cluster_filters.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,2162 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpy2jxg5my/galaxy-dev\n-Clonage dans \'/tmp/tmpy2jxg5my/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'ectory/000/3/working/clusterFilters_abundance.biom" ] ; then cp "/tmp/tmp4i61keb6/job_working_directory/000/3/working/clusterFilters_abundance.biom" "/tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_b5364850-68bb-461a-b125-24ecdcdf39e6.dat" ; fi; \n-if [ -f "/tmp/tmp4i61keb6/job_working_directory/000/3/working/clusterFilters_sequences.fasta" ] ; then cp "/tmp/tmp4i61keb6/job_working_directory/000/3/working/clusterFilters_sequences.fasta" "/tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_75e83388-0c36-442d-9fc7-8c8fa84cf623.dat" ; fi; \n-if [ -f "/tmp/tmp4i61keb6/job_working_directory/000/3/working/excluded.tsv" ] ; then cp "/tmp/tmp4i61keb6/job_working_directory/000/3/working/excluded.tsv" "/tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_55fc8909-8bc8-4643-8782-c6bf1d2f8aed.dat" ; fi; \n-if [ -f "/tmp/tmp4i61keb6/job_working_directory/000/3/working/report.html" ] ; then cp "/tmp/tmp4i61keb6/job_working_directory/000/3/working/report.html" "/tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_a3ea094e-a03b-4dbc-9e34-3a3fc2305df8.dat" ; fi; cd \'/tmp/tmp4i61keb6/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-04 14:54:58,327 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] (3) executing job script: /tmp/tmp4i61keb6/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-04 14:55:04,592 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 268056\n-galaxy.jobs.runners.local DEBUG 2023-05-04 14:55:04,592 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmp4i61keb6/job_working_directory/000/3/galaxy_3.sh\n-galaxy.jobs DEBUG 2023-05-04 14:55:04,624 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_b5364850-68bb-461a-b125-24ecdcdf39e6.dat to /tmp/tmp4i61keb6/files/b/5/3/dataset_b5364850-68bb-461a-b125-24ecdcdf39e6.dat\n-galaxy.jobs DEBUG 2023-05-04 14:55:04,625 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_75e83388-0c36-442d-9fc7-8c8fa84cf623.dat to /tmp/tmp4i61keb6/files/7/5/e/dataset_75e83388-0c36-442d-9fc7-8c8fa84cf623.dat\n-galaxy.jobs DEBUG 2023-05-04 14:55:04,625 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_55fc8909-8bc8-4643-8782-c6bf1d2f8aed.dat to /tmp/tmp4i61keb6/files/5/5/f/dataset_55fc8909-8bc8-4643-8782-c6bf1d2f8aed.dat\n-galaxy.jobs DEBUG 2023-05-04 14:55:04,625 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp4i61keb6/job_working_directory/000/3/outputs/galaxy_dataset_a3ea094e-a03b-4dbc-9e34-3a3fc2305df8.dat to /tmp/tmp4i61keb6/files/a/3/e/dataset_a3ea094e-a03b-4dbc-9e34-3a3fc2305df8.dat\n-galaxy.model.metadata DEBUG 2023-05-04 14:55:04,651 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.model.metadata DEBUG 2023-05-04 14:55:04,661 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 4\n-galaxy.model.metadata DEBUG 2023-05-04 14:55:04,669 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 5\n-galaxy.model.metadata DEBUG 2023-05-04 14:55:04,687 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 6\n-\n-galaxy.jobs DEBUG 2023-05-04 14:55:04,800 [pN:main.1,p:267936,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (182.302 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_cluster_filters (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/cluster_stats.log --- a/test-data/cluster_stats.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,994 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpp7deq3n5/galaxy-dev\n-Clonage dans \'/tmp/tmpp7deq3n5/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vdar'..b'e DEBUG 2023-04-26 12:35:28,108 [pN:main.1,p:216363,tN:WSGI_0] Created 1 job(s) for tool FROGS_cluster_stats request (152.333 ms)\n-\n-galaxy.jobs.mapper DEBUG 2023-04-26 12:35:28,731 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: planemo_dest\n-galaxy.jobs.handler DEBUG 2023-04-26 12:35:28,755 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to planemo_runner runner\n-galaxy.jobs DEBUG 2023-04-26 12:35:28,885 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: planemo_dest)\n-galaxy.jobs DEBUG 2023-04-26 12:35:28,915 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /tmp/tmpp7deq3n5/job_working_directory/000/2\n-galaxy.jobs.runners DEBUG 2023-04-26 12:35:28,960 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] Job [2] queued (204.437 ms)\n-galaxy.jobs.handler INFO 2023-04-26 12:35:28,990 [pN:main.1,p:216363,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n-galaxy.jobs DEBUG 2023-04-26 12:35:29,141 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] Job wrapper for Job [2] prepared (109.168 ms)\n-galaxy.tool_util.deps DEBUG 2023-04-26 12:35:29,143 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] Using dependency frogs version 4.1.0 of type conda\n-galaxy.tool_util.deps DEBUG 2023-04-26 12:35:29,143 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] Using dependency frogs version 4.1.0 of type conda\n-galaxy.jobs.command_factory INFO 2023-04-26 12:35:29,178 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] Built script [/tmp/tmpp7deq3n5/job_working_directory/000/2/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; cluster_stats.py --input-biom \'/tmp/tmpp7deq3n5/files/2/3/c/dataset_23cfcc4a-dba9-4b62-881a-962d04f6a0e2.dat\' --output-file \'/tmp/tmpp7deq3n5/job_working_directory/000/2/outputs/galaxy_dataset_06305cb4-045f-438d-8d0b-6dc224e89466.dat\']\n-\n-galaxy.jobs.runners DEBUG 2023-04-26 12:35:29,249 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpp7deq3n5/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpp7deq3n5/job_working_directory/000/2/galaxy_2.ec; \n-if [ -f "/tmp/tmpp7deq3n5/job_working_directory/000/2/working/summary.html" ] ; then cp "/tmp/tmpp7deq3n5/job_working_directory/000/2/working/summary.html" "/tmp/tmpp7deq3n5/job_working_directory/000/2/outputs/galaxy_dataset_06305cb4-045f-438d-8d0b-6dc224e89466.dat" ; fi; cd \'/tmp/tmpp7deq3n5/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-26 12:35:29,264 [pN:main.1,p:216363,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmpp7deq3n5/job_working_directory/000/2/galaxy_2.sh\n-galaxy.web_stack DEBUG 2023-04-26 12:35:29,279 [pN:main.1,p:216424,tN:Thread-9] server_name set to: main.1\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_cluster_stats (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/databases/frogs_picrust2_default_dir.loc --- a/test-data/databases/frogs_picrust2_default_dir.loc Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,37 +0,0 @@ -# Copyright (C) 2022 INRA -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. -# -# -#This is a sample file that enables tools FROGS_frogsfunc_placeseqs to place -#studies sequences (i.e. OTUs) into a reference tree. -# -#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult -#PICRUSt2 documentation to find out where they are located in your environment. -# -#If you are not comfortable with picrust2 command lines, just create .loc files -#with EXAMPLE FOR TEST files remembering to replace <PATH_TO> with the real path. -# -#<identifiant> <marker_gene> <path_to_default_dir> -# -#default dir must contain these files: -# -#-rw-rw-r-- 1 vdarbot vdarbot 31922081 avril 1 2021 pro_ref.fna -#-rwxrwxr-x 1 vdarbot vdarbot 272826 avril 1 2021 pro_ref.hmm -#-rwxrwxr-x 1 vdarbot vdarbot 116 avril 1 2021 pro_ref.model -#-rwxrwxr-x 1 vdarbot vdarbot 1707 avril 1 2021 pro_ref.raxml_info -#-rwxrwxr-x 1 vdarbot vdarbot 600048 avril 1 2021 pro_ref.tre -# -# EXAMPLE FOR TEST : -picrust2_default_dir_16S 16S ${__HERE__}/frogs_picrust2_db/prokaryotic/pro_ref/ ${__HERE__}/frogs_picrust2_db/prokaryiotic/pro_ref/16S_counts.txt.gz sepp \ No newline at end of file |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/databases/frogs_picrust2_functions.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_picrust2_functions.loc Tue Jun 13 06:59:09 2023 +0000 |
b |
@@ -0,0 +1,39 @@ +# Copyright (C) 2022 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_frogsfunc_copynumbers to predict +#the copy number of gene families present in the predicted genome for OTU, +# given a tree and a set of known trait values (FROGS_frogsfunc_placeseqs). +# +#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult +#PICRUSt2 documentation to find out where they are located in your environment. +# +#If you are not comfortable with picrust2 command lines, just create .loc files +#with EXAMPLE FOR TEST files remembering to replace <PATH_TO> with the real path. +# +#<marker_gene> <db> <picrust2_input_marker> <picrust2_input_function> <picrust_version> +# +#With 16S data, PICRUSt2 only takes the dname of the database as input (for exemple EC). +#With ITS and 18S data, you have to specify the path of marke gene counts files. +# +# EXAMPLE FOR TEST : +16S EC EC EC 2.5.1 +16S KO KO KO 2.5.1 +16S PFAM PFAM PFAM 2.5.1 +16S COG COG COG 2.5.1 +16S TIGRFAM TIGRFAM TIGRFAM 2.5.1 +16S PHENO PHENO PHENO 2.5.1 +ITS EC ${__HERE__}/frogs_picrust2_db/prokaryotic/16S_test.txt.gz ${__HERE__}/frogs_picrust2_db/prokaryotic/ec_test.txt.gz 2.5.1 \ No newline at end of file |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/databases/frogs_picrust2_marker_table.loc --- a/test-data/databases/frogs_picrust2_marker_table.loc Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,39 +0,0 @@ -# Copyright (C) 2022 INRA -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. -# -# -#This is a sample file that enables tools FROGS_frogsfunc_copynumbers to predict -#the copy number of gene families present in the predicted genome for OTU, -# given a tree and a set of known trait values (FROGS_frogsfunc_placeseqs). -# -#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult -#PICRUSt2 documentation to find out where they are located in your environment. -# -#If you are not comfortable with picrust2 command lines, just create .loc files -#with EXAMPLE FOR TEST files remembering to replace <PATH_TO> with the real path. -# -#<marker_gene> <db> <picrust2_input_marker> <picrust2_input_function> -# -#With 16S data, PICRUSt2 only takes the dname of the database as input (for exemple EC). -#With ITS and 18S data, you have to specify the path of marke gene counts files. -# -# EXAMPLE FOR TEST : -16S EC EC EC -16S KO KO KO -16S PFAM PFAM PFAM -16S COG COG COG -16S TIGRFAM TIGRFAM TIGRFAM -16S PHENO PHENO PHENO -ITS EC ${__HERE__}/frogs_picrust2_db/prokaryotic/16S_test.txt.gz ${__HERE__}/frogs_picrust2_db/prokaryotic/ec_test.txt.gz \ No newline at end of file |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/databases/frogs_picrust2_pathway_map.loc --- a/test-data/databases/frogs_picrust2_pathway_map.loc Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,32 +0,0 @@ -# Copyright (C) 2022 INRA -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. -# -# -#This is a sample file that enables tools FROGS_frogsfunc_pathways to map pathways to reactions. -#The default mapfile maps MetaCyc reactions to prokaryotic MetaCyc pathways. -# -#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult -#PICRUSt2 documentation to find out where they are located in your environment. -# -#If you are not comfortable with picrust2 command lines, just create .loc files -#with EXAMPLE FOR TEST files remembering to replace <PATH_TO> with the real path. -# -#<db_id> <db_name> <marker_gene> <path_to_mapfiles> -# -#First column will be the visible name in galaxy. -# -# -# EXAMPLE FOR TEST : -pro_metacyc_pathway Metacyc 16S ${__HERE__}/frogs_picrust2_db/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt \ No newline at end of file |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/databases/frogs_picrust2_pathways.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_picrust2_pathways.loc Tue Jun 13 06:59:09 2023 +0000 |
b |
@@ -0,0 +1,32 @@ +# Copyright (C) 2022 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_frogsfunc_pathways to map pathways to reactions. +#The default mapfile maps MetaCyc reactions to prokaryotic MetaCyc pathways. +# +#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult +#PICRUSt2 documentation to find out where they are located in your environment. +# +#If you are not comfortable with picrust2 command lines, just create .loc files +#with EXAMPLE FOR TEST files remembering to replace <PATH_TO> with the real path. +# +#<db_id> <db_name> <marker_gene> <path_to_mapfiles> +# +#First column will be the visible name in galaxy. +# +# +# EXAMPLE FOR TEST : +pro_metacyc_pathway Metacyc 16S ${__HERE__}/frogs_picrust2_db/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt 2.5.1 \ No newline at end of file |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/databases/frogs_picrust2_placeseqs.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/databases/frogs_picrust2_placeseqs.loc Tue Jun 13 06:59:09 2023 +0000 |
b |
@@ -0,0 +1,37 @@ +# Copyright (C) 2022 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_frogsfunc_placeseqs to place +#studies sequences (i.e. OTUs) into a reference tree. +# +#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult +#PICRUSt2 documentation to find out where they are located in your environment. +# +#If you are not comfortable with picrust2 command lines, just create .loc files +#with EXAMPLE FOR TEST files remembering to replace <PATH_TO> with the real path. +# +#<identifiant> <marker_gene> <path_to_default_dir> <path_to_marker_copy_numbers> <placement_tool> <frogs_version> +# +#default dir must contain these files: +# +#-rw-rw-r-- 1 vdarbot vdarbot 31922081 avril 1 2021 pro_ref.fna +#-rwxrwxr-x 1 vdarbot vdarbot 272826 avril 1 2021 pro_ref.hmm +#-rwxrwxr-x 1 vdarbot vdarbot 116 avril 1 2021 pro_ref.model +#-rwxrwxr-x 1 vdarbot vdarbot 1707 avril 1 2021 pro_ref.raxml_info +#-rwxrwxr-x 1 vdarbot vdarbot 600048 avril 1 2021 pro_ref.tre +# +# EXAMPLE FOR TEST : +picrust2_default_dir_16S 16S ${__HERE__}/frogs_picrust2_db/prokaryotic/pro_ref/ ${__HERE__}/frogs_picrust2_db/prokaryiotic/16S_counts.txt.gz sepp 2.5.1 \ No newline at end of file |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/deseq_peepro.log --- a/test-data/deseq_peepro.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,3082 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpyujvgsy0/galaxy-dev\n-Clonage dans \'/tmp/tmpyujvgsy0/galaxy-dev\'...\n-fait.\n-Mise \xc3\xa0 jour des fichiers: 36% (2247/6176)\rMise \xc3\xa0 jour des fichiers: 37% (2286/6176)\rMise \xc3\xa0 jour des fichiers: 38% (2347/6176)\rMise \xc3\xa0 jour des fichiers: 39% (2409/6176)\rMise \xc3\xa0 jour des fichiers: 40% (2471/6176)\rMise \xc3\xa0 jour des fichiers: 41% (2533/6176)\rMise \xc3\xa0 jour des fichiers: 42% (2594/6176)\rMise \xc3\xa0 jour des fichiers: 43% (2656/6176)\rMise \xc3\xa0 jour des fichiers: 44% (2718/6176)\rMise \xc3\xa0 jour des fichiers: 45% (2780/6176)\rMise \xc3\xa0 jour des fichiers: 46% (2841/6176)\rMise \xc3\xa0 jour des fichiers: 47% (2903/6176)\rMise \xc3\xa0 jour des fichiers: 48% (2965/6176)\rMise \xc3\xa0 jour des fichiers: 49% (3027/6176)\rMise \xc3\xa0 jour des fichiers: 50% (3088/6176)\rMise \xc3\xa0 jour des fichiers: 51% (3150/6176)\rMise \xc3\xa0 jour des fichiers: 52% (3212/6176)\rMise \xc3\xa0 jour des fichiers: 53% (3274/6176)\rMise \xc3\xa0 jour des fichiers: 54% (3336/6176)\rMise \xc3\xa0 jour des fichiers: 55% (3397/6176)\rMise \xc3\xa0 jour des fichiers: 56% (3459/6176)\rMise \xc3\xa0 jour des fichiers: 57% (3521/6176)\rMise \xc3\xa0 jour des fichiers: 58% (3583/6176)\rMise \xc3\xa0 jour des fichiers: 59% (3644/6176)\rMise \xc3\xa0 jour des fichiers: 60% (3706/6176)\rMise \xc3\xa0 jour des fichiers: 61% (3768/6176)\rMise \xc3\xa0 jour des fichiers: 62% (3830/6176)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6176)\rMise \xc3\xa0 jour des fichiers: 64% (3953/6176)\rMise \xc3\xa0 jour des fichiers: 65% (4015/6176)\rMise \xc3\xa0 jour des fichiers: 66% (4077/6176)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6176)\rMise \xc3\xa0 jour des fichiers: 68% (4200/6176)\rMise \xc3\xa0 jour des fichiers: 69% (4262/6176)\rMise \xc3\xa0 jour des fichiers: 70% (4324/6176)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6176)\rMise \xc3\xa0 jour des fichiers: 72% (4447/6176)\rMise \xc3\xa0 jour des fichiers: 73% (4509/6176)\rMise \xc3\xa0 jour des fichiers: 74% (4571/6176)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6176)\rMise \xc3\xa0 jour des fichiers: 76% (4694/6176)\rMise \xc3\xa0 jour des fichiers: 77% (4756/6176)\rMise \xc3\xa0 jour des fichiers: 78% (4818/6176)\rMise \xc3\xa0 jour des fichiers: 79% (4880/6176)\rMise \xc3\xa0 jour des fichiers: 80% (4941/6176)\rMise \xc3\xa0 jour des fichiers: 81% (5003/6176)\rMise \xc3\xa0 jour des fichiers: 82% (5065/6176)\rMise \xc3\xa0 jour des fichiers: 83% (5127/6176)\rMise \xc3\xa0 jour des fichiers: 84% (5188/6176)\rMise \xc3\xa0 jour des fichiers: 85% (5250/6176)\rMise \xc3\xa0 jour des fichiers: 86% (5312/6176)\rMise \xc3\xa0 jour des fichiers: 87% (5374/6176)\rMise \xc3\xa0 jour des fichiers: 88% (5435/6176)\rMise \xc3\xa0 jour des fichiers: 89% (5497/6176)\rMise \xc3\xa0 jour des fichiers: 90% (5559/6176)\rMise \xc3\xa0 jour des fichiers: 91% (5621/6176)\rMise \xc3\xa0 jour des fichiers: 92% (5682/6176)\rMise \xc3\xa0 jour des fichiers: 93% (5744/6176)\rMise \xc3\xa0 jour des fichiers: 94% (5806/6176)\rMise \xc3\xa0 jour des fichiers: 95% (5868/6176)\rMise \xc3\xa0 jour des fichiers: 96% (5929/6176)\rMise \xc3\xa0 jour des fichiers: 97% (5991/6176)\rMise \xc3\xa0 jour des fichiers: 98% (6053/6176)\rMise \xc3\xa0 jour des fichiers: 99% (6115/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176), fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n'..b' conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; deseq2_preprocess.py --analysis \'ASV\' --data \'/tmp/tmpo3qialyz/files/4/d/0/dataset_4d055b7e-a677-4b2e-a94d-84315f492786.dat\' --out-Rdata \'/tmp/tmpo3qialyz/job_working_directory/000/2/outputs/galaxy_dataset_d6606cce-2817-40a6-b852-b36cda5f4b83.dat\' --var \'EnvType\']\n-galaxy.jobs.runners DEBUG 2023-05-08 22:41:21,914 [pN:main.1,p:15544,tN:LocalRunner.work_thread-2] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpo3qialyz/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpo3qialyz/job_working_directory/000/2/galaxy_2.ec; \n-if [ -f "/tmp/tmpo3qialyz/job_working_directory/000/2/working/asv_dds.Rdata" ] ; then cp "/tmp/tmpo3qialyz/job_working_directory/000/2/working/asv_dds.Rdata" "/tmp/tmpo3qialyz/job_working_directory/000/2/outputs/galaxy_dataset_d6606cce-2817-40a6-b852-b36cda5f4b83.dat" ; fi; cd \'/tmp/tmpo3qialyz/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-08 22:41:21,925 [pN:main.1,p:15544,tN:LocalRunner.work_thread-2] (2) executing job script: /tmp/tmpo3qialyz/job_working_directory/000/2/galaxy_2.sh\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/deseq_visu.log --- a/test-data/deseq_visu.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,3098 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp7m6i1hb3/galaxy-dev\n-Clonage dans \'/tmp/tmp7m6i1hb3/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'OUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-be12999d9200037f8d53a21d6bb1a9a3530bc477fb4b35557938fb47596c6182\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-be12999d9200037f8d53a21d6bb1a9a3530bc477fb4b35557938fb47596c6182\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-be12999d9200037f8d53a21d6bb1a9a3530bc477fb4b35557938fb47596c6182\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; deseq2_visualisation.py --analysis \'ASV\' --abundanceData \'/tmp/tmpyx331lwu/files/8/5/1/dataset_851a201e-e1f3-4b5e-9a79-4bc7f915445a.dat\' --dds \'/tmp/tmpyx331lwu/files/d/1/7/dataset_d17130c9-7af8-48c6-b974-117aa3b44993.dat\' --var \'EnvType\' --mod1 \'BoeufHache\' --mod2 \'SaumonFume\' --padj 0.05 --html \'/tmp/tmpyx331lwu/job_working_directory/000/3/outputs/galaxy_dataset_092b5619-cb69-4cfa-b0fd-001ed2fc3e8b.dat\']\n-\n-galaxy.jobs.runners DEBUG 2023-05-08 22:38:59,172 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] (3) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpyx331lwu/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpyx331lwu/job_working_directory/000/3/galaxy_3.ec; \n-if [ -f "/tmp/tmpyx331lwu/job_working_directory/000/3/working/report.nb.html" ] ; then cp "/tmp/tmpyx331lwu/job_working_directory/000/3/working/report.nb.html" "/tmp/tmpyx331lwu/job_working_directory/000/3/outputs/galaxy_dataset_092b5619-cb69-4cfa-b0fd-001ed2fc3e8b.dat" ; fi; cd \'/tmp/tmpyx331lwu/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-08 22:38:59,183 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] (3) executing job script: /tmp/tmpyx331lwu/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-08 22:39:22,776 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 14485\n-galaxy.jobs.runners.local DEBUG 2023-05-08 22:39:22,776 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmpyx331lwu/job_working_directory/000/3/galaxy_3.sh\n-galaxy.jobs DEBUG 2023-05-08 22:39:22,818 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpyx331lwu/job_working_directory/000/3/outputs/galaxy_dataset_092b5619-cb69-4cfa-b0fd-001ed2fc3e8b.dat to /tmp/tmpyx331lwu/files/0/9/2/dataset_092b5619-cb69-4cfa-b0fd-001ed2fc3e8b.dat\n-galaxy.model.metadata DEBUG 2023-05-08 22:39:22,854 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.jobs DEBUG 2023-05-08 22:39:22,925 [pN:main.1,p:5194,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (113.531 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGSSTAT_DESeq2_Visualisation (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/deseq_visu_2.log --- a/test-data/deseq_visu_2.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,3068 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpbk65hbs9/galaxy-dev\n-Clonage dans \'/tmp/tmpbk65hbs9/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'emjm7d3ebaca4c817601cecc54647923eb4cf260b28adaacb06a74b65ed18ce0abac/__r-base@4.1.2\'\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-26 08:41:12,915 [pN:main.1,p:194555,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda install -y --strict-channel-priority --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmplt0jfs0b/deps/_cache/15115056 --file /tmp/tmplt0jfs0b/tmp/jobdepsut_nemjm7d3ebaca4c817601cecc54647923eb4cf260b28adaacb06a74b65ed18ce0abac/__r-base@4.1.2\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-26 08:41:18,923 [pN:main.1,p:194555,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda install -y --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmplt0jfs0b/deps/_cache/15115056 --file /tmp/tmplt0jfs0b/tmp/jobdepsut_nemjm7d3ebaca4c817601cecc54647923eb4cf260b28adaacb06a74b65ed18ce0abac/__r-base@4.1.2\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-26 08:41:25,333 [pN:main.1,p:194555,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda clean --tarballs -y\n-\n-galaxy.jobs.runners ERROR 2023-04-26 08:41:26,387 [pN:main.1,p:194555,tN:LocalRunner.work_thread-2] (3) Failure preparing job\n-Traceback (most recent call last):\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 262, in prepare_job\n- job_wrapper.runner_command_line = self.build_command_line(\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 301, in build_command_line\n- return build_command(\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 81, in build_command\n- __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n- if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n- self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n- return self.app.toolbox.dependency_manager.dependency_shell_commands(\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n- self.build_cache(requirements, **kwds)\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n- self.build_environment()\n- File "/tmp/tmplt0jfs0b/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n- raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n-galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n-galaxy.jobs DEBUG 2023-04-26 08:41:26,401 [pN:main.1,p:194555,tN:LocalRunner.work_thread-2] fail(): Moved /tmp/tmplt0jfs0b/job_working_directory/000/3/outputs/galaxy_dataset_08b8588d-8f12-440b-af76-49f93442c1fb.dat to /tmp/tmplt0jfs0b/files/0/8/b/dataset_08b8588d-8f12-440b-af76-49f93442c1fb.dat\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGSSTAT_DESeq2_Visualisation (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/filters.tsv --- a/test-data/filters.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
b'@@ -1,74921 +0,0 @@\n-#comment\tseed_id\tobservation_name\tobservation_sum\t01_subsample\t02_subsample\t03_subsample\n-no data\t01_54\tCluster_1\t1561\t512\t515\t534\n-no data\t01_92546\tCluster_2\t1556\t508\t512\t536\n-no data\t01_59\tCluster_3\t1550\t514\t502\t534\n-no data\t01_81\tCluster_4\t1564\t503\t515\t546\n-no data\t01_25\tCluster_5\t1544\t521\t550\t473\n-no data\t01_74803\tCluster_6\t1631\t512\t574\t545\n-no data\t01_38\tCluster_7\t1533\t509\t492\t532\n-no data\t01_90\tCluster_8\t1523\t526\t484\t513\n-no data\t01_97858\tCluster_9\t1571\t526\t494\t551\n-no data\t01_259\tCluster_10\t1519\t511\t529\t479\n-no data\t01_90304\tCluster_11\t1505\t469\t520\t516\n-no data\t01_22\tCluster_12\t1610\t542\t531\t537\n-no data\t01_94\tCluster_13\t1576\t527\t543\t506\n-no data\t01_76\tCluster_14\t1534\t495\t511\t528\n-no data\t01_60934\tCluster_15\t1565\t508\t527\t530\n-no data\t01_85419\tCluster_16\t1564\t535\t512\t517\n-no data\t01_54589\tCluster_17\t1502\t508\t504\t490\n-no data\t01_40\tCluster_18\t1516\t490\t531\t495\n-no data\t01_66\tCluster_19\t1465\t499\t490\t476\n-no data\t01_51488\tCluster_20\t1518\t526\t498\t494\n-no data\t01_54706\tCluster_21\t1520\t514\t507\t499\n-no data\t01_155\tCluster_22\t1523\t504\t483\t536\n-no data\t01_101\tCluster_23\t1500\t510\t472\t518\n-no data\t01_10\tCluster_24\t1530\t515\t500\t515\n-no data\t01_97506\tCluster_25\t1530\t491\t506\t533\n-no data\t01_151\tCluster_26\t1516\t494\t513\t509\n-no data\t01_108\tCluster_27\t1573\t536\t490\t547\n-no data\t01_71661\tCluster_28\t1545\t545\t507\t493\n-no data\t01_201\tCluster_29\t1537\t498\t515\t524\n-no data\t01_66997\tCluster_30\t1565\t525\t530\t510\n-no data\t01_190\tCluster_31\t1530\t511\t550\t469\n-no data\t01_96725\tCluster_32\t1546\t509\t522\t515\n-no data\t01_103\tCluster_33\t1597\t508\t544\t545\n-no data\t01_67\tCluster_34\t1499\t480\t504\t515\n-no data\t01_76743\tCluster_35\t1507\t525\t499\t483\n-no data\t01_222\tCluster_36\t1591\t536\t534\t521\n-no data\t01_19\tCluster_37\t1576\t499\t538\t539\n-no data\t01_264\tCluster_38\t1525\t473\t528\t524\n-no data\t01_91964\tCluster_39\t1512\t518\t508\t486\n-no data\t01_67210\tCluster_40\t1572\t534\t524\t514\n-no data\t01_91819\tCluster_41\t1529\t518\t517\t494\n-no data\t01_69140\tCluster_42\t1580\t540\t524\t516\n-no data\t01_65\tCluster_43\t1516\t497\t505\t514\n-no data\t01_85242\tCluster_44\t1531\t511\t518\t502\n-no data\t01_60\tCluster_45\t1584\t530\t513\t541\n-no data\t01_91485\tCluster_46\t1535\t507\t530\t498\n-no data\t01_410\tCluster_47\t1532\t499\t513\t520\n-no data\t01_86\tCluster_48\t544\t177\t203\t164\n-no data\t01_88865\tCluster_49\t245\t80\t83\t82\n-FROGS_combined\t01_71070_FROGS_combined\tCluster_50_FROGS_combined\t1597\t526\t518\t553\n-no data\t01_210\tCluster_51\t83\t22\t28\t33\n-no data\t01_1953\tCluster_52\t59\t26\t16\t17\n-no data\t01_4641\tCluster_53\t45\t17\t12\t16\n-no data\t01_3904\tCluster_54\t37\t9\t13\t15\n-no data\t01_67609\tCluster_55\t10\t2\t6\t2\n-no data\t01_97159\tCluster_56\t3\t1\t1\t1\n-FROGS_combined\t01_10004_FROGS_combined\tCluster_57_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10005_FROGS_combined\tCluster_58_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10008_FROGS_combined\tCluster_59_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10010_FROGS_combined\tCluster_60_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10018_FROGS_combined\tCluster_61_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10020_FROGS_combined\tCluster_62_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10029_FROGS_combined\tCluster_63_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10031_FROGS_combined\tCluster_64_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10032_FROGS_combined\tCluster_65_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10038_FROGS_combined\tCluster_66_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10039_FROGS_combined\tCluster_67_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_1003_FROGS_combined\tCluster_68_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10041_FROGS_combined\tCluster_69_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10043_FROGS_combined\tCluster_70_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10044_FROGS_combined\tCluster_71_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10046_FROGS_combined\tCluster_72_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10047_FROGS_combined\tCluster_73_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10051_FROGS_combined\tCluster_74_FROGS_combined\t1\t1\t0\t0\n-FROGS_combined\t01_10052_FROGS_combined\tCluster_75_FROGS_combined\t1\t1\t0\t0\n-'..b'mbined\tCluster_74870_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_98143_FROGS_combined\tCluster_74871_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_98144_FROGS_combined\tCluster_74872_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_98146_FROGS_combined\tCluster_74873_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_98148_FROGS_combined\tCluster_74874_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9814_FROGS_combined\tCluster_74875_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_98159_FROGS_combined\tCluster_74876_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_98161_FROGS_combined\tCluster_74877_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9820_FROGS_combined\tCluster_74878_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9823_FROGS_combined\tCluster_74879_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9824_FROGS_combined\tCluster_74880_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9826_FROGS_combined\tCluster_74881_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9830_FROGS_combined\tCluster_74882_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9834_FROGS_combined\tCluster_74883_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9835_FROGS_combined\tCluster_74884_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9841_FROGS_combined\tCluster_74885_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9848_FROGS_combined\tCluster_74886_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9862_FROGS_combined\tCluster_74887_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9866_FROGS_combined\tCluster_74888_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9872_FROGS_combined\tCluster_74889_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9874_FROGS_combined\tCluster_74890_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9880_FROGS_combined\tCluster_74891_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9882_FROGS_combined\tCluster_74892_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9885_FROGS_combined\tCluster_74893_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9886_FROGS_combined\tCluster_74894_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9895_FROGS_combined\tCluster_74895_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9900_FROGS_combined\tCluster_74896_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9904_FROGS_combined\tCluster_74897_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9911_FROGS_combined\tCluster_74898_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9913_FROGS_combined\tCluster_74899_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9917_FROGS_combined\tCluster_74900_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9923_FROGS_combined\tCluster_74901_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9925_FROGS_combined\tCluster_74902_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9927_FROGS_combined\tCluster_74903_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_992_FROGS_combined\tCluster_74904_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9930_FROGS_combined\tCluster_74905_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9935_FROGS_combined\tCluster_74906_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9939_FROGS_combined\tCluster_74907_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_994_FROGS_combined\tCluster_74908_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9950_FROGS_combined\tCluster_74909_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9955_FROGS_combined\tCluster_74910_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9958_FROGS_combined\tCluster_74911_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9960_FROGS_combined\tCluster_74912_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9968_FROGS_combined\tCluster_74913_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9973_FROGS_combined\tCluster_74914_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9974_FROGS_combined\tCluster_74915_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9975_FROGS_combined\tCluster_74916_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9978_FROGS_combined\tCluster_74917_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9981_FROGS_combined\tCluster_74918_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9985_FROGS_combined\tCluster_74919_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9986_FROGS_combined\tCluster_74920_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_9999_FROGS_combined\tCluster_74921_FROGS_combined\t1\t0\t0\t1\n-FROGS_combined\t03_999_FROGS_combined\tCluster_74922_FROGS_combined\t1\t0\t0\t1\n' |
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diff -r b2967b704d6b -r f479218f3736 test-data/frogsfun --- a/test-data/frogsfun Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,3 +0,0 @@ -git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch '+refs/*:refs/*' -git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true -git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1 |
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diff -r b2967b704d6b -r f479218f3736 test-data/frogsfunc.tsv --- a/test-data/frogsfunc.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,11 +0,0 @@ -#blast_taxonomy blast_subject blast_perc_identity blast_perc_query_coverage blast_evalue blast_aln_length seed_id observation_name observation_sum SC1703-104_TTGCCC-B6TML_L001_R SC1703-105_CAGTCT-B6TML_L001_R SC1703-106_TTAAAT-B6TML_L001_R SC1703-107_AATTGC-B6TML_L001_R SC1703-108_ACTCGA-B6TML_L001_R SC1703-109_GTTACC-B6TML_L001_R SC1703-110_CAGATG-B6TML_L001_R SC1703-125_TCGCGC-B6TML_L001_R SC1703-126_TAACTT-B6TML_L001_R SC1703-127_CTGTAA-B6TML_L001_R SC1703-128_CCATTG-B6TML_L001_R SC1703-129_TAGGCT-B6TML_L001_R SC1703-130_TTCTTG-B6TML_L001_R SC1703-131_CCGACC-B6TML_L001_R SC1703-132_TTAGCT-B6TML_L001_R SC1703-133_CAGAGC-B6TML_L001_R SC1703-134_AATATG-B6TML_L001_R SC1703-135_TGAGCA-B6TML_L001_R SC1703-136_AATCAC-B6TML_L001_R SC1703-137_GGTAGC-B6TML_L001_R SC1703-138_CTCTCG-B6TML_L001_R SC1703-145_AGCGAC-B6TML_L001_R SC1703-146_GCCAAG-B6TML_L001_R SC1703-147_AGGTTC-B6TML_L001_R SC1703-148_TTTTTC-B6TML_L001_R SC1703-149_GTCGTG-B6TML_L001_R SC1703-150_GCTATC-B6TML_L001_R SC1703-151_TATGCG-B6TML_L001_R SC1703-41_TCGTTC-B6TML_L001_R SC1703-42_GCGATG-B6TML_L001_R SC1703-43_ATATAA-B6TML_L001_R SC1703-44_ATACTG-B6TML_L001_R SC1703-45_GGAGAG-B6TML_L001_R SC1703-46_ACGAGA-B6TML_L001_R SC1703-47_ATTACA-B6TML_L001_R SC1703-48_TGATTT-B6TML_L001_R SC1703-49_GGGGTG-B6TML_L001_R SC1703-50_ACAAAA-B6TML_L001_R SC1703-51_CTCCAG-B6TML_L001_R SC1703-52_GGTGTT-B6TML_L001_R SC1703-53_CGGGAG-B6TML_L001_R SC1703-54_TGGTAG-B6TML_L001_R SC1703-62_TGCGGG-B6TML_L001_R SC1703-63_TCTATG-B6TML_L001_R SC1703-64_GGACGG-B6TML_L001_R SC1703-65_AGAGGG-B6TML_L001_R SC1703-66_ATGAAC-B6TML_L001_R SC1703-67_TACCTG-B6TML_L001_R SC1703-68_CTAGAG-B6TML_L001_R SC1703-83_CTTGCA-B6TML_L001_R SC1703-84_CATGTT-B6TML_L001_R SC1703-85_TGGATT-B6TML_L001_R SC1703-86_AACGCA-B6TML_L001_R SC1703-87_TTCGAG-B6TML_L001_R SC1703-88_AAGCTA-B6TML_L001_R SC1703-89_AGTTTG-B6TML_L001_R SC1703-90_TCCCCA-B6TML_L001_R SC1703-91_AACTAG-B6TML_L001_R SC1703-92_GTTCGC-B6TML_L001_R SC1703-93_TGCCTT-B6TML_L001_R SC1703-94_ATAAGA-B6TML_L001_R SC1703-95_CACACT-B6TML_L001_R SC1703-96_ACAGTT-B6TML_L001_R -Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Oscillibacter;unknown species HQ785790.1.1449 100.0 100.0 0.0 403 M02944:219:000000000-B6TML:1:1102:9099:12653 Cluster_1 243473 233 1305 1338 1495 598 348 395 2874 7160 25 6914 9935 15 5834 3173 2776 3139 3049 7358 3516 4819 89 768 158 205 63 204 72 4631 496 2803 1551 6231 1344 9366 7343 4415 1522 7335 5823 3464 5127 225 1457 465 425 578 445 271 3593 3408 11535 45 12854 4777 5248 8442 12633 5259 13924 9587 10678 8315 -Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Multi-affiliation multi-subject 100.0 100.0 0.0 426 M02944:219:000000000-B6TML:1:1102:5178:4304 Cluster_2 217042 398 1359 2720 3700 2166 548 2786 713 2851 3309 3405 2875 1547 4031 9781 4123 1986 1190 1897 3920 5053 719 2183 280 986 970 1069 165 5551 3806 9913 7876 3738 11421 5678 2313 3986 9454 1609 2163 1639 756 1408 3566 1938 1035 2739 3614 1705 4964 5597 3497 6844 6126 3565 3108 896 4885 3192 8005 4534 5326 3865 -Bacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;Eisenbergiella;unknown species multi-subject 99.75 100.0 0.0 401 M02944:219:000000000-B6TML:1:1102:25966:6564 Cluster_3 185228 842 1141 1162 1488 659 566 1822 1699 2709 2202 2769 1114 1806 2064 6555 5217 5265 20805 2725 6685 7949 4948 88 1572 3705 1466 1032 723 1617 1202 1266 2912 2020 842 2817 1706 4674 1892 1659 937 1226 2938 160 89 824 87 186 326 1490 2422 756 1769 1907 2959 1271 1191 5254 7123 12594 4108 7510 8390 6326 -Bacteria;Firmicutes;Clostridia;Clostridia vadinBB60 group;unknown family;unknown genus;unknown species GQ175436.1.1437 99.5 100.0 0.0 404 M02944:219:000000000-B6TML:1:1102:23486:4021 Cluster_4 113087 2280 676 1035 2733 1837 698 1118 17 30 7 28 10 7 5 2944 1092 1795 590 3034 913 1707 1311 1733 600 1012 393 1199 2003 5 1 4 41 6 9 18 6823 329 2262 7796 12328 7331 7710 2401 1809 1770 1331 8170 1071 845 9 10 10 30 18 12 17 3928 3449 1847 4401 2077 2536 1876 -Bacteria;Firmicutes;Clostridia;Clostridia vadinBB60 group;unknown family;unknown genus;gut metagenome CDZB01072114.19608.21101 99.01 100.0 0.0 404 M02944:219:000000000-B6TML:1:1114:7531:19741 Cluster_5 104097 14 16 18 11 49 60 44 227 7500 22187 17526 19048 11102 20612 0 0 94 77 0 2 39 1 1 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 2 1 5369 1 3 2 33 2 2 3 27 8 10 -Bacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species DQ456366.1.1454 100.0 100.0 0.0 401 M02944:219:000000000-B6TML:1:1102:12645:4964 Cluster_6 102648 3028 7155 7405 9799 4656 1759 2455 51 39 37 78 47 13 19 2668 2347 288 558 432 900 5393 1507 2756 3386 3607 2661 4604 2104 5 7 3 4 4 2 11 108 5 4 21 13 87 16 5819 610 1198 5003 6177 2239 5907 38 596 27 86 18 35 18 224 1154 2566 389 83 163 256 -Bacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Multi-affiliation multi-subject 100.0 100.0 0.0 402 M02944:219:000000000-B6TML:1:1102:25163:5970 Cluster_7 100935 1148 1468 1044 1396 552 612 1846 13 13 15 35 9 24 21 2666 728 4407 3321 9514 1597 2373 969 372 97 697 42 836 399 1 2 6 8 6 7 4 5184 1406 2379 1471 4165 2616 473 1876 1757 3013 1270 2225 1771 3610 41 20 32 76 34 22 11 15266 4545 2580 2981 1403 638 3822 -Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;unknown genus;Clostridium sp. multi-subject 99.5 100.0 0.0 404 M02944:219:000000000-B6TML:1:2118:16716:22396 Cluster_10 52413 2 4 7 19 4 7 7 290 369 3062 948 1596 231 1769 824 152 165 190 350 57 344 1 0 1 9 0 0 0 1634 963 3978 1161 398 15 1884 278 2075 333 629 1036 1579 4682 26 0 0 0 1 0 1 717 1213 4106 167 1136 1806 513 58 995 5041 610 160 3817 993 -Bacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species multi-subject 99.75 100.0 0.0 401 M02944:219:000000000-B6TML:1:1102:10609:2758 Cluster_11 49142 762 2421 812 1403 859 973 2543 107 152 233 186 639 85 364 177 222 525 249 311 947 411 355 114 736 720 257 940 314 358 720 41 22 727 348 205 49 18 176 152 31 48 376 1781 6486 2989 4222 3170 3299 2726 167 434 198 453 281 304 295 266 269 274 179 61 134 66 -Bacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Multi-affiliation multi-subject 100.0 100.0 0.0 404 M02944:219:000000000-B6TML:1:1102:14141:20035 Cluster_12 53185 175 168 505 260 140 338 316 1055 491 4500 1006 448 1647 1191 323 682 771 510 839 1232 708 11 198 26 224 32 50 11 559 263 281 2647 71 526 875 1022 612 103 269 371 382 271 358 869 296 348 586 368 627 1384 1800 613 3138 1499 978 3175 1861 1951 1888 1655 1355 911 1416 |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/frogsfunc_function.biom --- a/test-data/frogsfunc_function.biom Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1 +0,0 @@\n-{"id": null, "format": "Biological Observation Matrix 1.0.0", "format_url": "http://biom-format.org", "type": "OTU table", "generated_by": "swarm", "date": "2018-10-04T16:37:49", "rows": [{"id": "Cluster_1", "metadata": {"blast_taxonomy": ["Bacteria", "Firmicutes", "Clostridia", "Oscillospirales", "Oscillospiraceae", "Oscillibacter", "unknown species"], "seed_id": "M02944:219:000000000-B6TML:1:1102:9099:12653", "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Bacteria", "Firmicutes", "Clostridia", "Oscillospirales", "Oscillospiraceae", "Oscillibacter", "unknown species"], "evalue": "0.0", "aln_length": 403, "perc_query_coverage": 100.0, "subject": "HQ785790.1.1449"}], "NSTI": "0.033280000000000004", "picrust2_affiliations": "Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter;Oscillibacter_sp.", "blast_picrust_ref_perc_identity": "99.26", "blast_picrust_ref_perc_query_coverage": "100.0"}}, {"id": "Cluster_2", "metadata": {"blast_taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Multi-affiliation"], "seed_id": "M02944:219:000000000-B6TML:1:1102:5178:4304", "blast_affiliations": [{"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "LXJJ02000010.3161.4631"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli S88"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CU928161.4443202.4444743"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CU651637.2709763.2711303"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli O157:H7"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP033605.4932246.4933797"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Shigella flexneri"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP033510.2312050.2313603"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli O32:H37 str. P4"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "AJQW01000057.1.1280"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP032515.4680373.4681924"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "CP032265.2506313.2507866"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "Escherichia coli DEC8C"], "evalue": "0.0", "aln_length": 426, "perc_query_coverage": 100.0, "subject": "AIGH01000069.160053.161583"}, {"perc_identity": 100.0, "taxonomy": ["Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Escherichia-Shigella", "unknown species"], "eval'..b' [5, 23, 3386], [5, 24, 3607], [5, 25, 2661], [5, 26, 4604], [5, 27, 2104], [5, 28, 5], [5, 29, 7], [5, 30, 3], [5, 31, 4], [5, 32, 4], [5, 33, 2], [5, 34, 11], [5, 35, 108], [5, 36, 5], [5, 37, 4], [5, 38, 21], [5, 39, 13], [5, 40, 87], [5, 41, 16], [5, 42, 5819], [5, 43, 610], [5, 44, 1198], [5, 45, 5003], [5, 46, 6177], [5, 47, 2239], [5, 48, 5907], [5, 49, 38], [5, 50, 596], [5, 51, 27], [5, 52, 86], [5, 53, 18], [5, 54, 35], [5, 55, 18], [5, 56, 224], [5, 57, 1154], [5, 58, 2566], [5, 59, 389], [5, 60, 83], [5, 61, 163], [5, 62, 256], [6, 0, 1148], [6, 1, 1468], [6, 2, 1044], [6, 3, 1396], [6, 4, 552], [6, 5, 612], [6, 6, 1846], [6, 7, 13], [6, 8, 13], [6, 9, 15], [6, 10, 35], [6, 11, 9], [6, 12, 24], [6, 13, 21], [6, 14, 2666], [6, 15, 728], [6, 16, 4407], [6, 17, 3321], [6, 18, 9514], [6, 19, 1597], [6, 20, 2373], [6, 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[9, 57, 1951], [9, 58, 1888], [9, 59, 1655], [9, 60, 1355], [9, 61, 911], [9, 62, 1416]], "shape": [10, 63], "matrix_type": "sparse"}\n\\ No newline at end of file\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/frogsfunc_function.fasta --- a/test-data/frogsfunc_function.fasta Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,20 +0,0 @@ ->Cluster_1 -TGGGGAATATTGGGCAATGGACGCAAGTCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTTGTAAACTTCTTTTGTCAGGGAACAGTAGAAGAGGGTACCTGACGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGCAGCCGGGCCGGCAAGTCAGATGTGAAATCTGGAGGCTTAACCTCCAAACTGCATTTGAAACTGTTGGTCTTGAGTACCGGAGAGGTTATCGGAATTCCTTGTGTAGCGGTGAAATGCGTAGATATAAGGAAGAACACCAGTGGCGAAGGCGGATAACTGGACGGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAAC ->Cluster_2 -TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAAC ->Cluster_3 -TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGTGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGAGTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAAGCAAGTCTGGAGTGAAAACCCGGGGCTTAACCCCGGGATTGCTTTGGAAACTGTTTAACTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC ->Cluster_4 -TGGGGAATATTGGGCAATGGAGGCAACTCTGACCCAGCAACGCCGCGTGAATGATGAAGGTCTTCGGATTGTAAAGTTCTGTGACGGGGGACGAACACAATGACGGTACCCCGATAGCAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTAGCAAGTTGGCAGCGTAATTCCGGGGCTCAACTCCGGCGCTACTGCCAAAACTGTTGAACTTGAGTGCAGGAGGGGTAAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACATCGGTGGCGAAGGCGACTTACTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAAC ->Cluster_5 -TGGGGAATATTGGGCAATGGAGGGAACTCTGACCCAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATTGTAAAACTCTTTAAGCGGGGACGAAGAAAGTGACTGTACCCGCAGAATAAGCATCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGATGCAAGCGTTATCCGGAATGACTGGGCGTAAAGGGTGCGTAGGTGGTTTGCCAAGTTGGCAGCGTAATTCCGTGGCTTAACCGCGGAACTACTGCCAAAACTGGTAGGCTTGAGTGCGGCAGGGGTATGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAAGCGACATACTGGGCCGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAAC ->Cluster_6 -TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAACTGACGGTACCTGACTAAGAAGCACCGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATGTGCAAGTCTGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTAGATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC ->Cluster_7 -TAGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGGAGGATGACACTTTTCGGAGCGTAAACTCCTTTTCTTAGGGAAGAATTCTGACGGTACCTAAGGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGGGCGCGTAGGCGGATTATCAAGTCTCTTGTGAAATCTAATGGCTTAACCATTAAACTGCTTGGGAAACTGATAGTCTAGAGTGAGGGAGAGGCAGATGGAATTGGTGGTGTAGGGGTAAAATCCGTAGATATCACCAAGAATACCCATTGCGAAGGCGATCTGCTGGAACTCAACTGACGCTAAGGCGCGAAAGCGTGGGGAGCAAAC ->Cluster_10 -TGGGGAATATTGGGCAATGGGCGCAAGCCTGACCCAGCAACGCCGCGTGAAGGATGAAGGCTTTCGGGTTGTAAACTTCTTTTATTCGGGACGAAGCAAGTGACGGTACCGAATGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGACTGCAAGTCAGATGTGAAAACTATGGGCTCAACCCATAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCATAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAAC ->Cluster_11 -TGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCACCGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATAGGCAAGTCTGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTTTATCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC ->Cluster_12 -TGGGGAATATTGGGCAATGGGCGCAAGCCTGACCCAGCAACGCCGCGTGAAGGAAGAAGGCTTTCGGGTTGTAAACTTCTTTTGTCGGGGACGAAACAAATGACGGTACCCGACGAATAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGATTGCAAGTCAGATGTGAAAACTGGGGGCTCAACCTCCAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAAC |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/frogsfunc_function.log --- a/test-data/frogsfunc_function.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1162 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp4273t1nv/galaxy-dev\n-Clonage dans \'/tmp/tmp4273t1nv/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (23.0.1)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.40.0)\n-\n-[notice] A new release of pip is available: 23.0.1 -> 23.1.2\n-[notice] To update, run: pip install --upgrade pip\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 9)) ('..b'b_working_directory/000/5/galaxy_5.sh\n-galaxy.jobs DEBUG 2023-05-19 16:19:37,325 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_db725e94-3a7d-41ec-adaa-1244567389ce.dat to /tmp/tmp4273t1nv/files/d/b/7/dataset_db725e94-3a7d-41ec-adaa-1244567389ce.dat\n-galaxy.jobs DEBUG 2023-05-19 16:19:37,330 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_2122339b-71c0-4022-b021-90db95a8c0e1.dat to /tmp/tmp4273t1nv/files/2/1/2/dataset_2122339b-71c0-4022-b021-90db95a8c0e1.dat\n-galaxy.jobs DEBUG 2023-05-19 16:19:37,332 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_6336af35-9eb4-4d0c-8d57-8003aadbd4bf.dat to /tmp/tmp4273t1nv/files/6/3/3/dataset_6336af35-9eb4-4d0c-8d57-8003aadbd4bf.dat\n-galaxy.jobs DEBUG 2023-05-19 16:19:37,334 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_9caba39b-ecaa-41a8-9a90-0a0cb84b1f98.dat to /tmp/tmp4273t1nv/files/9/c/a/dataset_9caba39b-ecaa-41a8-9a90-0a0cb84b1f98.dat\n-galaxy.jobs DEBUG 2023-05-19 16:19:37,336 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_74c9f54d-b000-4304-afa4-acbb8875462d.dat to /tmp/tmp4273t1nv/files/7/4/c/dataset_74c9f54d-b000-4304-afa4-acbb8875462d.dat\n-galaxy.jobs DEBUG 2023-05-19 16:19:37,340 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_7fc1784c-aa05-4115-a182-e6d08ac9cd05.dat to /tmp/tmp4273t1nv/files/7/f/c/dataset_7fc1784c-aa05-4115-a182-e6d08ac9cd05.dat\n-galaxy.jobs DEBUG 2023-05-19 16:19:37,344 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_5777a52e-e1f9-483b-bcdc-b52d82e4ef3a.dat to /tmp/tmp4273t1nv/files/5/7/7/dataset_5777a52e-e1f9-483b-bcdc-b52d82e4ef3a.dat\n-galaxy.jobs DEBUG 2023-05-19 16:19:37,347 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmp4273t1nv/job_working_directory/000/5/outputs/galaxy_dataset_c0387e32-e757-49fd-a2bf-56cfaf491599.dat to /tmp/tmp4273t1nv/files/c/0/3/dataset_c0387e32-e757-49fd-a2bf-56cfaf491599.dat\n-galaxy.model.metadata DEBUG 2023-05-19 16:19:37,417 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 5\n-galaxy.model.metadata DEBUG 2023-05-19 16:19:37,430 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 6\n-galaxy.model.metadata DEBUG 2023-05-19 16:19:37,442 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 7\n-galaxy.model.metadata DEBUG 2023-05-19 16:19:37,453 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 8\n-galaxy.model.metadata DEBUG 2023-05-19 16:19:37,469 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 9\n-galaxy.model.metadata DEBUG 2023-05-19 16:19:37,483 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 10\n-galaxy.model.metadata DEBUG 2023-05-19 16:19:37,496 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 11\n-galaxy.model.metadata DEBUG 2023-05-19 16:19:37,513 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 12\n-galaxy.jobs DEBUG 2023-05-19 16:19:37,721 [pN:main.1,p:349089,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 5 executed (422.874 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGSFUNC_step3_functions (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/frogsfunc_pathways_predictions.tsv --- a/test-data/frogsfunc_pathways_predictions.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
b'@@ -1,11 +0,0 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t0.0\t0.0\t1.018181818181818\t0.0\t0.0\t1.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t1.5\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0909090909090908\t1.0909090909090908\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0909090909090908\t1.024390243902439\t0.0\t0.0\t1.0\t1.1428571428571428\n-Cluster_6\t1.0769230769230769\t0.0\t0.0\t1.1612903225806452\t0.0\t0.0\t1.180327868852459\t1.2000000000000002\t1.1666666666666667\t0.0\t0.0\t0.0\t1.1764705882352942\t1.0909090909090908\t1.0\t1.0\t0.0\t1.2307692307692308\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.3333333333333333\t1.1764705882352942\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0769230769230769\t1.0\t1.2\t1.2307692307692308\t0.0\t0.0\t1.0769230769230769\t0.0\t0.0\t0.0\t1.105263157894737\t1.3333333333333333\t0.0\t0.0\t0.0\t0.0\t0.0\t1.3333333333333333\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1428571428571428\t1.0588235294117647\t0.0\t1.0\t1.25\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.1428571428571428\t0.0\t0.0\t1.0769230769230769\t1.0\t1.3333333333333333\t1.1764705882352942\t1.1764705882352942\t1.0645161290322582\t0.0\t0.0\t0.0\t1.0769230769230769\t0.0\t0.0\t0.0\t0.0\t0.0\t1.3333333333333333\t0.0\t0.0\t1.2413793103448276\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.153846153846154\t0.0\t0.0\t1.1111111111111112\t1.1428571428571428\t1.0\t0.0\t1.3333333333333333\t0.0\t1.0\t1.0\t1.1111111111111112\t0.0\t0.0\t1.1428571428571428\t0.0\t1.0\t0.0\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.2\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.4545454545454546\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.2307692307692308\t0.0\t1.4545454545454546\t1.2\t1.1428571428571428\t1.2\t0.0\t1.411764705882353\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1748251748251748\t0.0\t1.0\t1.105263157894737\t1.2000000000000002\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t1.3333333333333333\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.2\t1.2\t1.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0909090909090908\t1.05\t1.1111111111111112\t0.0\t0.0\t1.2307692307692308\n-Cluster_7\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.0\t0.0\t0.0\t1.1764705882352942\t1.0\t1.0\t0.0\t0.0\t1.0666666666666667\t1.0588235294117647\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.3333333333333333\t0.0\t1.0\t0.0\t0.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.3333333333333333\t0.0\t0.0\t1.0\t1.0\t0.0\t1.0\t1.25\t0.0\t1.0\t0.0\t0.0\t1.0\t0.0\t1.0909090909090908\t1.0526315789473684\t1.2903225806451613\t0.0\t1.0769230769230769\t1.0\t1.25\t1.1111111111111112\t1.1111111111111112\t0.0\t0.0\t1.0909090909090908\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1428571428571428\t0.0\t0.0\t1.2\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t1.1538461538461537\t1.2\t1.0909090909090908\t1.0769230769230769\t1.3124999999999998\t1.0\t1.0\t1.1428571428571428\t1.0\t0.0\t0.0\t1.2\t0.0\t0.0\t0.0\t1.0\t1.0\t1.0\t1.0\t0.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.0\t0.0\t0.0\t1.0\t1.0\t1.0\t1.2\t1.2\t0.0\t0.0\t1.0\t1.1428571428571428\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t1.0\t0.0\t1.4117647058823528\t1.2\t1.0\t1.2\t1.0909090909090908\t1.3846153846153844\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t1.0\t0.0\t0.0\t1.1428571428571428\t1.0\t1.0\t0.0\t1.1785714285714286\t0.0\t1.1111111111111112\t0.0\t0.0\t0.0\t0.0\t0.0\t1.1428571428571428\t0.0\t0.0\t0.0\t0.0\t0.0\t1.125\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t1.0909090909090908\t1.0909090909090908\t0.0\t0.0\t0.0\t1.12\t0.0\t1.0169491525423728\t0.0\t1.0\t0.0\t0.0\t1.0909090909090908\t0.0\t1.2\t1.0\t0.0\t1.1111111111111112\t0.0\t1.0\t1.1428571428571428\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/frogsfunc_pathways_strat.tsv --- a/test-data/frogsfunc_pathways_strat.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
b'@@ -1,53629 +0,0 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|
b |
diff -r b2967b704d6b -r f479218f3736 test-data/frogsfunc_pathways_summary.html --- a/test-data/frogsfunc_pathways_summary.html Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
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If not, see <http://www.gnu.org/licenses/>.\n--->\n-<html>\n-\t<head>\n-\t\t<title>FrogsFunc pathways (Step4)</title>\n-\t\t<meta charset="UTF-8">\n-\t\t<meta name="version" content="4.1.0">\n-\t\t<!-- CSS -->\n-\t\t<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.1/css/bootstrap.css"></link>\n-\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"></link>\n-\t\t<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">\n-\t\t<style type="text/css">\n-\t\t\t/*\n-\t\t\t * jDistrib 0.1.0 - CSS jDistrib Library\t\n-\t\t\t *\t\t \n-\t\t\t * Copyright (c) 2015 Escudie Frederic\n-\t\t\t * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.\n-\t\t\t */\n-\t\t\t#sunburst-graph{margin-left:auto;margin-right:auto}.jDistrib-walk-rank{height:100%;margin-right:2px;padding:8px;float:left;border-top-right-radius:7px;border-bottom-right-radius:7px;cursor:pointer;box-shadow:1px 1px 1px #555}.jDistrib-walk-rank-size{margin-left:5px;padding:4px;background-color:#FFF;color:#648a89;border-radius:9px;text-align:center;font-size:10px;font-family:sans-serif}.jDistrib-root-label{font-weight:700;cursor:pointer}.jDistrib-arc-label{cursor:pointer}.jDistrib-arc{cursor:pointer;stroke:#fff;fill-rule:evenodd}.jDistrib-tooltip{position:absolute;padding:10px;font:12px sans-serif;background:#8EADAC;border:0;border-radius:8px;pointer-events:none}.jDistrib-empty-details{color:#fff;background-color:#8EADAC;padding:15px;margin-bottom:20px;border:1px solid transparent;border-radius:4px}.jDistrib-table-details>tbody>tr:nth-of-type(2n+1){background-color:#F5F5F5}.jDistrib-table-details{border:1px solid #DDD;border-radius:8px;border-spacing:1px;border-collapse:separate}.jDistrib-table-details td,th{padding:2px 8px}.jDistrib-table-details .number{text-align:right}.jDistrib-export-toggle{height:30px;width:30px;padding:1px}.jDistrib-export-toggle div{background-color:#636363;border-radius:2px;height:3px;margin-top:2px;margin-bottom:2px}\n-\t\t</style>\n-\t\t<style type="text/css">\n-\t\t\t#js-alert {\n-\t\t\t\twidth: 90%;\n-\t\t\t\tmargin-right: auto;\n-\t\t\t\tmargin-left: auto;\n-\t\t\t}\n-\t\t\t#content {\n-\t\t\t\twidth: 90%;\n-\t\t\t\tmargin-right: auto;\n-\t\t\t\tmargin-left: auto;\n-\t\t\t}\n-\t\t\t.clear {\n-\t\t\t\tclear: both;\n-\t\t\t\theight: 0px;\n-\t\t\t\twidth: 100%;\n-\t\t\t\tfloat: none !important;\n-\t\t\t}\n-\t\t\t.page-item.active .page-link {\n-\t\t\t\tz-index: 1;\n-\t\t\t\tcolor: #fff;\n-\t\t\t\tbackground-color: #8EADAC;\n-\t\t\t\tborder-color: #8EADAC;\n-\t\t\t}\n-\t\t\t.btn {\n-\t\t\t\tcolor: #fff;\n-\t\t\t\tborder:#8EADAC;\n-\t\t\t\tbackground-color: #8EADAC;\n-\t\t\t}\n-\t\t\t.btn:focus, .btn:active {\n-\t\t\t\toutline: none !important;\n-\t\t\t\tbox-shadow: none !important;\n-\t\t\t}\n-\t\t\t.btn:hover{\n-\t\t\t\tcolor: #fff;\n-\t\t\t\tborder:#648a89;\n-\t\t\t\tbackground-color: #648a89;\n-\t\t\t}\n-\t\t\t.pb-2, .py-2 {\n-\t\t\t\tpadding-bottom: 1.5rem !important;\n-\t\t\t\tmargin-bottom: 2rem !important;\n-\t\t\t\tmargin-top: 4rem !important;\n-\t\t\t}\n-\t\t\t.pb-2-first{\n-\t\t\t\tpadding-bottom: 1.5rem !important;\n-\t\t\t\tmargin-bottom: 2rem !important;\n-\t\t\t\tmargin-top: 1rem !important;\n-\t\t\t}\n-\t\t\t.nav-tabs .nav-link.active, .nav-tabs .nav-item.show .nav-link{\n-\t\t\t\tcolor: #fff;\n-\t\t\t\tbackground-color: #8EADAF;\n-\t\t\t\tborder-color: #dee2e6 #dee2e6 #fff;\n-\t\t\t}\n-\t\t\ta {\n-\t\t\t\tcolor: #8EAEAF;\n-\t\t\t}\n-\t\t\ta:hover{\n-\t\t\t\tcolor:#648a89;\n-\t\t\t}\n-\t\t\t.page-link{\n-\t\t\t\tcolor: #8EAEAF;\n-\t\t\t}\n-\t\t\t'..b'15\\": 3287, \\"16\\": 1792, \\"17\\": 1121, \\"18\\": 1784, \\"19\\": 3247, \\"20\\": 4247, \\"21\\": 647, \\"22\\": 1722, \\"23\\": 261, \\"24\\": 865, \\"25\\": 751, \\"26\\": 924, \\"27\\": 161, \\"28\\": 4061, \\"29\\": 2381, \\"30\\": 6260, \\"31\\": 5173, \\"32\\": 2984, \\"33\\": 5284, \\"34\\": 4602, \\"35\\": 2155, \\"36\\": 3294, \\"37\\": 5859, \\"38\\": 1523, \\"39\\": 2040, \\"40\\": 1535, \\"41\\": 738, \\"42\\": 1256, \\"43\\": 2884, \\"44\\": 1631, \\"45\\": 932, \\"46\\": 2475, \\"47\\": 2650, \\"48\\": 1450, \\"49\\": 3650, \\"50\\": 4028, \\"51\\": 3113, \\"52\\": 5048, \\"53\\": 5083, \\"54\\": 2877, \\"55\\": 2619, \\"56\\": 876, \\"57\\": 4394, \\"58\\": 2946, \\"59\\": 6745, \\"60\\": 3954, \\"61\\": 4686, \\"62\\": 3434})\\"unknow\\")\\"Nucleic Acid Processing\\")\\"Macromolecule Modification\\")\\"root\\"" ;\n-\t\t\t/* This string is in newick extended format. The metadata is the count by sample (each sample is referenced by is index position in "samples_names"). */\n-\n-\t\t\t$(function() {\n-\t\t\t\t// Remove alert\n-\t\t\t\t$(\'#js-alert\').remove();\n-\t\t\t\t$(\'#content\').removeClass("hidden");\n-\n-\t\t\t\t// Load active tab\n-\t\t\t\ttaxBySample_load( "tax-distrib" );\n-\t\t\t\t\n-\t\t\t\t$(\'#filter-log\').append( table("Chimera detection by sample", table_categories, table_series) );\n-\t\t\t\t$(\'#filter-log table\').prop( \'id\', \'details-table\' );\n-\t\t\t\t$(\'#filter-log table\').DataTable({\n-\t\t\t\t\tdom: \t"<\'#details-csv-export\'><\'row\'<\'col-sm-5\'l><\'col-sm-7\'f>>" +\n-\t\t\t\t\t\t\t"<\'row\'<\'col-sm-12\'tr>>" +\n-\t\t\t\t\t\t\t"<\'row\'<\'col-sm-5\'i><\'col-sm-7\'p>>",\n-\t\t\t\t\t\'lengthMenu\': [[10, 25, 50, 100, -1], [10, 25, 50, 100, "All"]],\n-\t\t\t\t});\n-\t\t\t\t$(\'#details-csv-export\').html( \'<button class="btn"><span class="fa fa-download" aria-hidden="true"> CSV</span></button>\' );\n-\t\t\t\t$(\'#details-csv-export\').addClass( \'dataTables_filter\' );\n-\t\t\t\t$(\'#details-csv-export\').datatableExport({\n-\t\t\t\t\t\'table_id\': "details-table"\n-\t\t\t\t});\n-\t\t\t});\n-\t\t</script>\n-\t</head>\n-\t<body>\n-\t\t<!-- Alert -->\n-\t\t<p id="js-alert" class="alert alert-warning">\n-\t\t\tjavascript is needed to display data.<br />\n-\t\t\tIf you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n-\t\t</p>\n-\t\t\n-\t\t<!-- Content -->\n-\t\t<div id="content" class="hidden">\n-\n-\t\t\t<div id="tab-content" class="tab-content">\n-\t\t\t\t<div id="tax-distrib" role="tabpanel" class="tab-pane active">\n-\t \t\t<h2 class="pb-2 mt-4 mb-2 border-bottom">Pathway abundances per sample\n-\n-\t\t\t\t\t</h2>\n-\t\t\t\t\t<button id="display-global-sunburst" class="btn d-block mx-auto" data-toggle="modal" data-target="#sunburst-modal">\n-\t\t\t\t\t\t<span class="fa fa-pie-chart" aria-hidden="true"> Display global distribution</span>\n-\t\t\t\t\t</button>\n-\t\t\t\t\t<table id="taxBySample-table" class="table table-striped">\n-\t\t\t\t\t\t<thead>\n-\t\t\t\t\t\t</thead>\n-\t\t\t\t\t\t<tbody></tbody>\n-\t\t\t\t\t\t<tfoot>\n-\t\t\t\t\t\t\t<tr>\n-\t\t\t\t\t\t\t\t<th>\n-\t\t\t\t\t\t\t\t\t<button id="display-spl-sunburst" class="btn table-action" disabled data-toggle="modal" data-target="#sunburst-modal"><span class="fa fa-pie-chart" aria-hidden="true"> Display distribution</span></button>\n-\t\t\t\t\t\t\t\t</th>\n-\t\t\t\t\t\t\t</tr>\n-\t\t\t\t\t\t</tfoot>\n-\t\t\t\t\t</table>\n-\t\t\t\t</div>\n-\t\t\t<div class="modal" id="sunburst-modal" tabindex="-1" role="dialog" aria-hidden="true">\n-\t\t\t\t<div class="modal-dialog modal-lg">\n-\t\t\t\t\t<div class="modal-content">\n-\t\t\t\t\t\t<div class="modal-header">\n-\t\t\t\t\t\t\t<h6 class="modal-title">Pathways distribution</h6>\n-\t\t\t\t\t\t\t<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n-\t\t\t\t\t\t</div>\n-\t\t\t\t\t\t<div class="modal-body">\n-\t\t\t\t\t\t\t<div id="sunburst-walktrace"></div>\n-\t\t\t\t\t\t\t<div id="sunburst-graph"></div>\n-\t\t\t\t\t\t\t<div>\n-\t\t\t\t\t\t\t\t</br><h6>Detail on selected:</h6>\n-\t\t\t\t\t\t\t\t<div id="sunburst-detail"></div>\n-\t\t\t\t\t\t\t</div>\n-\t\t\t\t\t\t</div>\n-\t\t\t\t\t\t<div class="modal-footer">\n-\t\t\t\t\t\t\t<span id="sunburst-menu"></span>\n-\t\t\t\t\t\t\t<button type="button" class="btn btn-default" data-dismiss="modal"><span class="fa fa-close" aria-hidden="true"> Close</span> </button>\n-\t\t\t\t\t\t</div>\n-\t\t\t\t\t</div>\n-\t\t\t\t</div>\n-\t\t\t</div>\n-\t\t</div>\n-\t</body>\n-</html>\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/frogsfunc_pathways_unstrat.tsv --- a/test-data/frogsfunc_pathways_unstrat.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
b'@@ -1,251 +0,0 @@\n-classification\tdb_link\tobservation_name\tobservation_sum\tSC1703-104_TTGCCC-B6TML_L001_R\tSC1703-105_CAGTCT-B6TML_L001_R\tSC1703-106_TTAAAT-B6TML_L001_R\tSC1703-107_AATTGC-B6TML_L001_R\tSC1703-108_ACTCGA-B6TML_L001_R\tSC1703-109_GTTACC-B6TML_L001_R\tSC1703-110_CAGATG-B6TML_L001_R\tSC1703-125_TCGCGC-B6TML_L001_R\tSC1703-126_TAACTT-B6TML_L001_R\tSC1703-127_CTGTAA-B6TML_L001_R\tSC1703-128_CCATTG-B6TML_L001_R\tSC1703-129_TAGGCT-B6TML_L001_R\tSC1703-130_TTCTTG-B6TML_L001_R\tSC1703-131_CCGACC-B6TML_L001_R\tSC1703-132_TTAGCT-B6TML_L001_R\tSC1703-133_CAGAGC-B6TML_L001_R\tSC1703-134_AATATG-B6TML_L001_R\tSC1703-135_TGAGCA-B6TML_L001_R\tSC1703-136_AATCAC-B6TML_L001_R\tSC1703-137_GGTAGC-B6TML_L001_R\tSC1703-138_CTCTCG-B6TML_L001_R\tSC1703-145_AGCGAC-B6TML_L001_R\tSC1703-146_GCCAAG-B6TML_L001_R\tSC1703-147_AGGTTC-B6TML_L001_R\tSC1703-148_TTTTTC-B6TML_L001_R\tSC1703-149_GTCGTG-B6TML_L001_R\tSC1703-150_GCTATC-B6TML_L001_R\tSC1703-151_TATGCG-B6TML_L001_R\tSC1703-41_TCGTTC-B6TML_L001_R\tSC1703-42_GCGATG-B6TML_L001_R\tSC1703-43_ATATAA-B6TML_L001_R\tSC1703-44_ATACTG-B6TML_L001_R\tSC1703-45_GGAGAG-B6TML_L001_R\tSC1703-46_ACGAGA-B6TML_L001_R\tSC1703-47_ATTACA-B6TML_L001_R\tSC1703-48_TGATTT-B6TML_L001_R\tSC1703-49_GGGGTG-B6TML_L001_R\tSC1703-50_ACAAAA-B6TML_L001_R\tSC1703-51_CTCCAG-B6TML_L001_R\tSC1703-52_GGTGTT-B6TML_L001_R\tSC1703-53_CGGGAG-B6TML_L001_R\tSC1703-54_TGGTAG-B6TML_L001_R\tSC1703-62_TGCGGG-B6TML_L001_R\tSC1703-63_TCTATG-B6TML_L001_R\tSC1703-64_GGACGG-B6TML_L001_R\tSC1703-65_AGAGGG-B6TML_L001_R\tSC1703-66_ATGAAC-B6TML_L001_R\tSC1703-67_TACCTG-B6TML_L001_R\tSC1703-68_CTAGAG-B6TML_L001_R\tSC1703-83_CTTGCA-B6TML_L001_R\tSC1703-84_CATGTT-B6TML_L001_R\tSC1703-85_TGGATT-B6TML_L001_R\tSC1703-86_AACGCA-B6TML_L001_R\tSC1703-87_TTCGAG-B6TML_L001_R\tSC1703-88_AAGCTA-B6TML_L001_R\tSC1703-89_AGTTTG-B6TML_L001_R\tSC1703-90_TCCCCA-B6TML_L001_R\tSC1703-91_AACTAG-B6TML_L001_R\tSC1703-92_GTTCGC-B6TML_L001_R\tSC1703-93_TGCCTT-B6TML_L001_R\tSC1703-94_ATAAGA-B6TML_L001_R\tSC1703-95_CACACT-B6TML_L001_R\tSC1703-96_ACAGTT-B6TML_L001_R\n-Biosynthesis;Cofactor, Carrier, and Vitamin Biosynthesis;Carrier Biosynthesis;N10-formyl-tetrahydrofolate biosynthesis\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=1CMET2-PWY\t1CMET2-PWY\t927684.2471538748\t7771.848912803767\t14550.56118405238\t14189.010237139522\t19077.458595669184\t9601.022946604224\t5311.386445901301\t11110.576523303067\t6664.964283662128\t14870.437120519862\t23097.332579307542\t22031.236621795193\t23827.99465527487\t9806.627134895085\t23287.689938012827\t20429.965908030503\t14208.47891180511\t13781.717425098926\t27606.834603576273\t17210.526504232716\t16427.235674515236\t23681.543722473263\t8963.109791113597\t6184.111397445648\t6790.477955072719\t10434.626225582524\t5393.202105875216\t9062.985496500736\t4987.458116492045\t10426.069717385071\t5348.034776031318\t12388.318766690787\t12553.994229110722\t8232.398602010442\t7350.539029337016\t15310.744578228532\t16218.83884638255\t13935.99538740025\t9833.506810497332\t14817.531730158298\t15756.233557755957\t12009.111512405387\t18686.54504903672\t12512.194841079527\t13580.436537937787\t10058.849993394497\t12981.905680714932\t18708.86682059204\t10421.082233341867\t15643.757631411429\t10571.49725246205\t11118.016933906272\t17418.575398581615\t13156.490904856253\t17754.89241763858\t10505.979240405686\t12691.14745334794\t23526.30875474508\t28152.38824654989\t32493.719641021587\t25014.136835338017\t20562.932374517255\t27109.439631553272\t20473.344721293648\n-Superpathways;Superpathways;unknow;superpathway of chorismate metabolism\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ALL-CHORISMATE-PWY\tALL-CHORISMATE-PWY\t128140.7736287208\t320.9624175662686\t1008.2326990168227\t1770.9521088501856\t2409.985071960181\t1345.601504456415\t407.66948995230473\t1908.8945131820672\t386.6749672439121\t1510.7554024493686\t1742.1455656412725\t1823.574154404105\t1536.0729727867051\t824.0986751052706\t2140.3696695686417\t5894.59745908816\t2441.2962721364174\t1552.6774585477083\t958.4391811784636\t1554.421221739443\t2556.0138835679836\t3365.594269807512\t546.2193167293985\t1282.3103049666245\t186.222034596'..b'hesis (prokaryotic)\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=UBISYN-PWY\tUBISYN-PWY\t103858.1690088619\t283.8557548849694\t857.2970795672918\t1428.00671147494\t1933.5822973879115\t1055.6951674553789\t346.749906089441\t1604.9103272494349\t288.8943839261784\t1126.66296374311\t1250.0138278055124\t1352.6763149912217\t1138.2839079962312\t593.9631676031337\t1581.6698246873405\t4825.763957611481\t1918.211339708544\t1382.0521688734486\t849.0363208807887\t1416.6368513351201\t2091.8218480785467\t2766.4464531937388\t466.43374616245313\t1003.4002142043897\t144.56418551839175\t575.2255768716637\t387.8366722833915\t634.7686239480747\t115.54607556217086\t2143.0988381466377\t1438.7567516062481\t3772.72656113961\t2988.7500590323143\t1462.1963680616043\t4315.248308940894\t2217.7692399998714\t1616.2497725244123\t2079.7587226048186\t4583.913939648795\t1001.5227466875572\t1485.0154897292168\t1098.2365486353374\t443.93982932279005\t912.0770189625796\t1955.0142471356696\t1284.2867465943698\t663.3965325002138\t1637.7059942990818\t1969.172271496301\t1175.1063134585977\t1934.8767195491605\t2161.112299112384\t1395.894751669367\t2610.512427071326\t2418.3526042781864\t1399.0607103275108\t1219.447198492738\t701.250471758203\t3033.57279225788\t1929.7858215173665\t4239.384401677083\t2333.6501232288256\t2398.108049124061\t2419.2126691765907\n-Biosynthesis;Carbohydrate Biosynthesis;Sugar Biosynthesis;UDP-N-acetyl-D-glucosamine biosynthesis I\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=UDPNAGSYN-PWY\tUDPNAGSYN-PWY\t1048419.8001489481\t6766.185504471118\t8771.17856639686\t9838.869975430502\t13387.17483264015\t6965.613267497504\t4397.794425088211\t9144.41725220489\t7477.300760558702\t19856.18115016376\t38374.19163107772\t31552.329788421004\t34059.51260873622\t16946.075180330918\t34303.54705421636\t21739.28604694809\t14231.415431810892\t17678.16551755997\t30022.701373987325\t25860.874850954104\t17784.583873423988\t23562.17541791721\t8599.742818061677\t5452.131224175115\t4082.621368259923\t8474.65398358582\t3524.1465071684306\t5816.773924486878\t4396.328960374379\t11122.803115062992\t4908.896250726809\t11953.232802538503\t13198.701938812888\t10488.359217140394\t7324.001590255255\t17871.0743178017\t24240.136117777864\t15450.707038969818\t11872.529130435525\t20099.625689764853\t25782.92211487701\t17627.573699931796\t22009.10519394557\t8906.80965864585\t11264.633918349735\t9390.241208928634\t7104.597745127698\t17685.71369297843\t7963.064399862438\t11717.510669022933\t11235.358051195046\t11479.819870446734\t20009.349064343263\t16491.475983324548\t22200.452754216003\t11238.31905161429\t14997.63516144053\t37319.08720243839\t35322.406310496364\t34107.61845531864\t32391.292498843413\t25042.047369969645\t29879.379754193083\t25657.345814203323\n-Biosynthesis;Amino Acid Biosynthesis;Proteinogenic Amino Acid Biosynthesis;L-valine biosynthesis\thttps://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=VALSYN-PWY\tVALSYN-PWY\t1406181.5843505547\t10684.910156546483\t18976.923220449982\t18486.72420752998\t25290.373468875503\t12754.883404746864\t7156.599891624007\t14503.12004036198\t9094.285963847777\t25263.90262908061\t42551.78579183445\t38994.781352656624\t42285.80108355911\t19323.601876318047\t42002.79842228746\t29780.60846116226\t19703.198069940474\t22569.62039674206\t38989.61304862352\t32321.6757306435\t23335.073155163114\t33985.00912983194\t11694.978163174403\t8725.043001031105\t8335.694826572677\t13240.178673554536\t6538.382510741776\t11449.85685041585\t6930.363655053134\t14771.985665406823\t6743.192044422416\t16300.418836600396\t15653.732328803198\t14525.717183788292\t9593.72614590039\t23116.77181643358\t29660.906969471704\t20400.915099286296\t15414.24681153891\t25132.915122548573\t31632.994179303143\t21894.346102294094\t28386.107283144374\t16308.361958728472\t18609.91639148099\t14007.367568843936\t16395.507761486464\t27202.814905682022\t13608.517957005228\t20151.97585989198\t14143.581942644538\t14234.935612270985\t24860.894194913755\t18259.296360388158\t27745.870286889243\t14227.588190474917\t15995.258460700343\t45778.78628939491\t45322.76509773363\t44965.837757481444\t41081.327973799685\t32515.946190633553\t39655.429651332626\t32911.841167466635\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/frogsfunc_pathways_unstrat_per_seq.tsv --- a/test-data/frogsfunc_pathways_unstrat_per_seq.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
b'@@ -1,248 +0,0 @@\n-pathway\tSC1703-104_TTGCCC-B6TML_L001_R\tSC1703-105_CAGTCT-B6TML_L001_R\tSC1703-106_TTAAAT-B6TML_L001_R\tSC1703-107_AATTGC-B6TML_L001_R\tSC1703-108_ACTCGA-B6TML_L001_R\tSC1703-109_GTTACC-B6TML_L001_R\tSC1703-110_CAGATG-B6TML_L001_R\tSC1703-125_TCGCGC-B6TML_L001_R\tSC1703-126_TAACTT-B6TML_L001_R\tSC1703-127_CTGTAA-B6TML_L001_R\tSC1703-128_CCATTG-B6TML_L001_R\tSC1703-129_TAGGCT-B6TML_L001_R\tSC1703-130_TTCTTG-B6TML_L001_R\tSC1703-131_CCGACC-B6TML_L001_R\tSC1703-132_TTAGCT-B6TML_L001_R\tSC1703-133_CAGAGC-B6TML_L001_R\tSC1703-134_AATATG-B6TML_L001_R\tSC1703-135_TGAGCA-B6TML_L001_R\tSC1703-136_AATCAC-B6TML_L001_R\tSC1703-137_GGTAGC-B6TML_L001_R\tSC1703-138_CTCTCG-B6TML_L001_R\tSC1703-145_AGCGAC-B6TML_L001_R\tSC1703-146_GCCAAG-B6TML_L001_R\tSC1703-147_AGGTTC-B6TML_L001_R\tSC1703-148_TTTTTC-B6TML_L001_R\tSC1703-149_GTCGTG-B6TML_L001_R\tSC1703-150_GCTATC-B6TML_L001_R\tSC1703-151_TATGCG-B6TML_L001_R\tSC1703-41_TCGTTC-B6TML_L001_R\tSC1703-42_GCGATG-B6TML_L001_R\tSC1703-43_ATATAA-B6TML_L001_R\tSC1703-44_ATACTG-B6TML_L001_R\tSC1703-45_GGAGAG-B6TML_L001_R\tSC1703-46_ACGAGA-B6TML_L001_R\tSC1703-47_ATTACA-B6TML_L001_R\tSC1703-48_TGATTT-B6TML_L001_R\tSC1703-49_GGGGTG-B6TML_L001_R\tSC1703-50_ACAAAA-B6TML_L001_R\tSC1703-51_CTCCAG-B6TML_L001_R\tSC1703-52_GGTGTT-B6TML_L001_R\tSC1703-53_CGGGAG-B6TML_L001_R\tSC1703-54_TGGTAG-B6TML_L001_R\tSC1703-62_TGCGGG-B6TML_L001_R\tSC1703-63_TCTATG-B6TML_L001_R\tSC1703-64_GGACGG-B6TML_L001_R\tSC1703-65_AGAGGG-B6TML_L001_R\tSC1703-66_ATGAAC-B6TML_L001_R\tSC1703-67_TACCTG-B6TML_L001_R\tSC1703-68_CTAGAG-B6TML_L001_R\tSC1703-83_CTTGCA-B6TML_L001_R\tSC1703-84_CATGTT-B6TML_L001_R\tSC1703-85_TGGATT-B6TML_L001_R\tSC1703-86_AACGCA-B6TML_L001_R\tSC1703-87_TTCGAG-B6TML_L001_R\tSC1703-88_AAGCTA-B6TML_L001_R\tSC1703-89_AGTTTG-B6TML_L001_R\tSC1703-90_TCCCCA-B6TML_L001_R\tSC1703-91_AACTAG-B6TML_L001_R\tSC1703-92_GTTCGC-B6TML_L001_R\tSC1703-93_TGCCTT-B6TML_L001_R\tSC1703-94_ATAAGA-B6TML_L001_R\tSC1703-95_CACACT-B6TML_L001_R\tSC1703-96_ACAGTT-B6TML_L001_R\n-1CMET2-PWY\t7523.245840080972\t12668.56882591093\t12655.536831983805\t17900.17344129555\t9354.903846153846\t4783.831113360324\t9575.02089068826\t3815.298471659919\t4996.802236842105\t12669.20141700405\t6589.848684210527\t5056.822226720648\t4874.638552631579\t7270.75798582996\t17400.690900809717\t11624.659777327935\t9803.775556680162\t23542.722813765184\t8685.309321862349\t12632.444979757085\t19009.724048582993\t8517.258997975709\t5967.141842105263\t6692.740748987853\t9987.728380566801\t5381.057044534413\t8588.617267206477\t5381.073127530364\t6398.173694331984\t4640.9401720647775\t9313.197479757086\t10516.17571862348\t4625.653087044535\t6114.265688259109\t8176.182074898787\t11165.840587044533\t9373.164615384616\t8285.544139676113\t11204.46367408907\t15629.832236842105\t11382.90572874494\t16357.444585020243\t11623.22354251012\t11495.278734817814\t7975.653846153846\t11865.911943319838\t19957.38410931174\t8921.708137651822\t12874.476325910931\t7001.268866396761\t7479.402469635628\t8205.011528340081\t9289.710384615384\t8637.769483805669\t6027.73467611336\t7347.624746963562\t12519.90221659919\t17439.18988866397\t26173.384615384617\t14838.317419028339\t13346.239483805668\t18210.432803643725\t12819.135991902835\n-ALL-CHORISMATE-PWY\t153.30755555555552\t523.4666666666666\t1047.7075555555555\t1425.1813333333332\t834.311111111111\t211.0853333333333\t1073.1297777777777\t274.64088888888887\t1098.159111111111\t1274.5777777777776\t1311.5555555555554\t1107.4035555555554\t595.8853333333333\t1552.6853333333333\t3767.492444444444\t1588.1146666666664\t764.9777777777778\t458.3742222222222\t730.6924444444444\t1509.9297777777776\t1946.3368888888886\t276.95199999999994\t840.863111111111\t107.84799999999998\t379.79644444444443\t373.6257777777777\t411.75911111111105\t63.55555555555555\t2138.1591111111106\t1466.0186666666666\t3818.3368888888886\t3033.7146666666663\t1439.822222222222\t4399.2\t2187.0853333333334\t890.9333333333333\t1535.3519999999999\t3641.5368888888884\t619.7591111111111\t833.1555555555555\t631.3146666666667\t291.2\t542.3368888888888\t1373.5742222222223\t746.4888888888888\t398.66666666666663\t1055.0222222222221\t1392.063111111111\t656.7368'..b'77777777\t8622.966666666667\t10960.366666666669\t12928.144444444446\t20216.666666666668\t13171.477777777778\t13072.222222222223\t13895.922222222223\t13266.300000000001\t11600.0\t13620.0\t23156.666666666668\t11011.855555555556\t16829.25555555556\t4812.966666666668\t4090.7444444444445\t3557.4111111111115\t5370.366666666667\t5946.666666666666\t3147.0333333333333\t2853.3333333333335\t28040.744444444448\t20187.033333333333\t23250.000000000004\t16362.58888888889\t14050.366666666667\t15151.477777777778\t15149.25555555556\n-UBISYN-PWY\t149.25374999999997\t509.6249999999999\t1020.0037499999997\t1387.4962499999997\t812.2499999999999\t205.50374999999994\t1044.7537499999999\t267.3787499999999\t1069.12125\t1240.8749999999998\t1276.8749999999998\t1078.12125\t580.1287499999999\t1511.6287499999999\t3667.8712499999992\t1546.1212499999997\t744.7499999999999\t446.2537499999999\t711.3712499999999\t1470.0037499999999\t1894.8712499999995\t269.6287499999999\t818.6287499999997\t104.99624999999997\t369.75374999999997\t363.7462499999999\t400.8712499999999\t61.874999999999986\t2081.6212499999997\t1427.2537499999999\t3717.3712499999992\t2953.4962499999992\t1401.7499999999998\t4282.874999999999\t2129.25375\t867.3749999999998\t1494.7537499999999\t3545.2462499999992\t603.3712499999999\t811.1249999999999\t614.6212499999999\t283.49999999999994\t527.9962499999999\t1337.2537499999999\t726.7499999999999\t388.12499999999994\t1027.1249999999998\t1355.2537499999999\t639.3712499999999\t1861.5037499999996\t2098.87875\t1311.3787499999999\t2566.4962499999992\t2297.2499999999995\t1336.8712499999997\t1165.4999999999998\t336.00374999999997\t1831.8712499999995\t1196.9999999999998\t3001.8712499999992\t1700.2462499999997\t1997.2462499999995\t1449.3712499999997\n-UDPNAGSYN-PWY\t5070.257264957265\t5501.025641025641\t6776.795726495726\t9112.366666666667\t4824.2991452991455\t3273.9666666666667\t6993.086324786325\t7818.693162393162\t19969.999145299145\t39108.17094017094\t31802.64957264957\t33810.65726495726\t17558.735897435898\t34546.428205128206\t20529.973504273505\t13065.879487179487\t17379.786324786324\t29649.667521367523\t25619.742735042735\t17064.93247863248\t20736.323931623934\t7610.684615384615\t4227.445299145299\t2591.7\t6510.111965811966\t2397.1017094017093\t3782.3068376068377\t3284.4957264957266\t11233.922222222223\t4681.55641025641\t12376.939316239317\t14698.494871794872\t10209.290598290598\t7660.846153846154\t18212.197435897437\t24549.128205128203\t15787.607692307693\t12127.170085470085\t20106.69145299145\t25946.264957264957\t17704.571794871794\t21835.384615384617\t6035.631623931624\t8438.12905982906\t7472.854700854701\t4300.410256410257\t13527.752136752137\t5800.752991452991\t8295.400854700856\t11815.368376068376\t11635.812820512821\t20162.804273504273\t17370.349572649575\t22730.11965811966\t11468.289743589745\t15460.03418803419\t37607.47094017094\t35058.56324786325\t32862.1452991453\t32811.04188034188\t25570.178632478634\t30141.89658119658\t26041.170085470087\n-VALSYN-PWY\t10493.26008097166\t18114.42975708502\t17538.427807981494\t24299.95206477733\t12347.22252747253\t6839.5179757085025\t14060.156842105265\t8301.335066512434\t23226.683325621747\t40408.800520532095\t36295.74080393291\t39797.066061307116\t18526.1242799306\t39299.75418160787\t27699.511029496818\t18102.76886639676\t20842.452834008098\t36749.61233661076\t30152.256257952577\t21340.393713128975\t31280.365396182766\t11585.735558126084\t8285.955511856564\t8216.809207634471\t12975.998918449972\t6475.501457489879\t11277.514239444767\t6912.8665413533845\t13219.19795835743\t6179.359097744361\t14503.301515326779\t14307.172249855408\t13086.19034123771\t8731.172874493926\t21075.620722961245\t28098.55078079815\t18320.630989010988\t14391.169126662811\t23980.13925390399\t30508.917611336034\t20848.853799884328\t26587.21029496819\t16010.884048582997\t17576.966356275305\t13568.65934065934\t15980.157056101792\t26811.59392712551\t13140.38842105263\t19612.266350491616\t12698.77870445344\t12888.994031231925\t23825.35108733372\t17154.210219780216\t25779.172267206475\t12972.169849624059\t14909.354106419894\t42739.30033545401\t41358.059323308276\t41096.249450549454\t37838.15397339503\t29334.287981492194\t35754.99243493348\t29885.954320416426\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/frogsfunc_placeseq.log --- a/test-data/frogsfunc_placeseq.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1944 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpr6jvdj77/galaxy-dev\n-Clonage dans \'/tmp/tmpr6jvdj77/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (23.0.1)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.40.0)\n-\n-[notice] A new release of pip is available: 23.0.1 -> 23.1.2\n-[notice] To update, run: pip install --upgrade pip\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 9)) ('..b'ctory.py", line 81, in build_command\n- __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n- File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n- if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n- File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n- self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n- File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n- return self.app.toolbox.dependency_manager.dependency_shell_commands(\n- File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n- self.build_cache(requirements, **kwds)\n- File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n- self.build_environment()\n- File "/tmp/tmpr6jvdj77/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n- raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n-galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n-galaxy.jobs DEBUG 2023-05-19 15:50:36,663 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_4d1ced49-69cd-4696-8d92-ce4a5967c293.dat to /tmp/tmpr6jvdj77/files/4/d/1/dataset_4d1ced49-69cd-4696-8d92-ce4a5967c293.dat\n-galaxy.jobs DEBUG 2023-05-19 15:50:36,664 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_642e9579-12ff-44c4-8eb5-e82b7de244a3.dat to /tmp/tmpr6jvdj77/files/6/4/2/dataset_642e9579-12ff-44c4-8eb5-e82b7de244a3.dat\n-galaxy.jobs DEBUG 2023-05-19 15:50:36,665 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_80f0d648-c925-4e66-b028-316c06951a95.dat to /tmp/tmpr6jvdj77/files/8/0/f/dataset_80f0d648-c925-4e66-b028-316c06951a95.dat\n-galaxy.jobs DEBUG 2023-05-19 15:50:36,666 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_ed4e7d62-8117-490e-8d85-a0b9b41fcbba.dat to /tmp/tmpr6jvdj77/files/e/d/4/dataset_ed4e7d62-8117-490e-8d85-a0b9b41fcbba.dat\n-galaxy.jobs DEBUG 2023-05-19 15:50:36,667 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_bcfc1b01-ff11-44b0-9338-5d13e4068d08.dat to /tmp/tmpr6jvdj77/files/b/c/f/dataset_bcfc1b01-ff11-44b0-9338-5d13e4068d08.dat\n-galaxy.jobs DEBUG 2023-05-19 15:50:36,669 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_c69b2d6d-7eee-4ced-9efe-5c87cb3bf3e4.dat to /tmp/tmpr6jvdj77/files/c/6/9/dataset_c69b2d6d-7eee-4ced-9efe-5c87cb3bf3e4.dat\n-galaxy.jobs DEBUG 2023-05-19 15:50:36,670 [pN:main.1,p:287121,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmpr6jvdj77/job_working_directory/000/3/outputs/galaxy_dataset_d4a40bbb-8eee-4697-b354-8e592d6be533.dat to /tmp/tmpr6jvdj77/files/d/4/a/dataset_d4a40bbb-8eee-4697-b354-8e592d6be533.dat\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGSFUNC_step1_placeseqs (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/log_chimera.txt --- a/test-data/log_chimera.txt Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1091 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpo_r_z575/galaxy-dev\n-Clonage dans \'/tmp/tmpo_r_z575/galaxy-dev\'...\n-fait.\n-Mise \xc3\xa0 jour des fichiers: 44% (2768/6175)\rMise \xc3\xa0 jour des fichiers: 45% (2779/6175)\rMise \xc3\xa0 jour des fichiers: 46% (2841/6175)\rMise \xc3\xa0 jour des fichiers: 47% (2903/6175)\rMise \xc3\xa0 jour des fichiers: 48% (2964/6175)\rMise \xc3\xa0 jour des fichiers: 49% (3026/6175)\rMise \xc3\xa0 jour des fichiers: 50% (3088/6175)\rMise \xc3\xa0 jour des fichiers: 51% (3150/6175)\rMise \xc3\xa0 jour des fichiers: 52% (3211/6175)\rMise \xc3\xa0 jour des fichiers: 53% (3273/6175)\rMise \xc3\xa0 jour des fichiers: 54% (3335/6175)\rMise \xc3\xa0 jour des fichiers: 55% (3397/6175)\rMise \xc3\xa0 jour des fichiers: 56% (3458/6175)\rMise \xc3\xa0 jour des fichiers: 57% (3520/6175)\rMise \xc3\xa0 jour des fichiers: 58% (3582/6175)\rMise \xc3\xa0 jour des fichiers: 59% (3644/6175)\rMise \xc3\xa0 jour des fichiers: 60% (3705/6175)\rMise \xc3\xa0 jour des fichiers: 60% (3759/6175)\rMise \xc3\xa0 jour des fichiers: 61% (3767/6175)\rMise \xc3\xa0 jour des fichiers: 62% (3829/6175)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6175)\rMise \xc3\xa0 jour des fichiers: 64% (3952/6175)\rMise \xc3\xa0 jour des fichiers: 65% (4014/6175)\rMise \xc3\xa0 jour des fichiers: 66% (4076/6175)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6175)\rMise \xc3\xa0 jour des fichiers: 68% (4199/6175)\rMise \xc3\xa0 jour des fichiers: 69% (4261/6175)\rMise \xc3\xa0 jour des fichiers: 70% (4323/6175)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6175)\rMise \xc3\xa0 jour des fichiers: 72% (4446/6175)\rMise \xc3\xa0 jour des fichiers: 73% (4508/6175)\rMise \xc3\xa0 jour des fichiers: 74% (4570/6175)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6175)\rMise \xc3\xa0 jour des fichiers: 76% (4693/6175)\rMise \xc3\xa0 jour des fichiers: 77% (4755/6175)\rMise \xc3\xa0 jour des fichiers: 78% (4817/6175)\rMise \xc3\xa0 jour des fichiers: 79% (4879/6175)\rMise \xc3\xa0 jour des fichiers: 80% (4940/6175)\rMise \xc3\xa0 jour des fichiers: 81% (5002/6175)\rMise \xc3\xa0 jour des fichiers: 82% (5064/6175)\rMise \xc3\xa0 jour des fichiers: 83% (5126/6175)\rMise \xc3\xa0 jour des fichiers: 84% (5187/6175)\rMise \xc3\xa0 jour des fichiers: 85% (5249/6175)\rMise \xc3\xa0 jour des fichiers: 86% (5311/6175)\rMise \xc3\xa0 jour des fichiers: 87% (5373/6175)\rMise \xc3\xa0 jour des fichiers: 88% (5434/6175)\rMise \xc3\xa0 jour des fichiers: 89% (5496/6175)\rMise \xc3\xa0 jour des fichiers: 90% (5558/6175)\rMise \xc3\xa0 jour des fichiers: 91% (5620/6175)\rMise \xc3\xa0 jour des fichiers: 92% (5681/6175)\rMise \xc3\xa0 jour des fichiers: 93% (5743/6175)\rMise \xc3\xa0 jour des fichiers: 94% (5805/6175)\rMise \xc3\xa0 jour des fichiers: 95% (5867/6175)\rMise \xc3\xa0 jour des fichiers: 96% (5928/6175)\rMise \xc3\xa0 jour des fichiers: 97% (5990/6175)\rMise \xc3\xa0 jour des fichiers: 98% (6052/6175)\rMise \xc3\xa0 jour des fichiers: 99% (6114/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175), fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual'..b'dat\' --out-abundance \'/tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_d8aea5cb-a5bf-45e6-80f9-c8a9c9c3c28b.dat\']\n-galaxy.jobs.runners DEBUG 2023-04-14 08:58:09,384 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] (3) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpo_r_z575/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpo_r_z575/job_working_directory/000/3/galaxy_3.ec; \n-if [ -f "/tmp/tmpo_r_z575/job_working_directory/000/3/working/non_chimera.fasta" ] ; then cp "/tmp/tmpo_r_z575/job_working_directory/000/3/working/non_chimera.fasta" "/tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_aea36576-9657-4334-90f0-9dce5336d078.dat" ; fi; \n-if [ -f "/tmp/tmpo_r_z575/job_working_directory/000/3/working/non_chimera_abundance.biom" ] ; then cp "/tmp/tmpo_r_z575/job_working_directory/000/3/working/non_chimera_abundance.biom" "/tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_d8aea5cb-a5bf-45e6-80f9-c8a9c9c3c28b.dat" ; fi; \n-if [ -f "/tmp/tmpo_r_z575/job_working_directory/000/3/working/report.html" ] ; then cp "/tmp/tmpo_r_z575/job_working_directory/000/3/working/report.html" "/tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_89d82b28-b154-4b39-9e19-48b26e4e974f.dat" ; fi; cd \'/tmp/tmpo_r_z575/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-14 08:58:09,418 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] (3) executing job script: /tmp/tmpo_r_z575/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-14 08:59:50,043 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 62985\n-galaxy.jobs.runners.local DEBUG 2023-04-14 08:59:50,044 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmpo_r_z575/job_working_directory/000/3/galaxy_3.sh\n-galaxy.jobs DEBUG 2023-04-14 08:59:50,130 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_aea36576-9657-4334-90f0-9dce5336d078.dat to /tmp/tmpo_r_z575/files/a/e/a/dataset_aea36576-9657-4334-90f0-9dce5336d078.dat\n-galaxy.jobs DEBUG 2023-04-14 08:59:50,132 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_d8aea5cb-a5bf-45e6-80f9-c8a9c9c3c28b.dat to /tmp/tmpo_r_z575/files/d/8/a/dataset_d8aea5cb-a5bf-45e6-80f9-c8a9c9c3c28b.dat\n-galaxy.jobs DEBUG 2023-04-14 08:59:50,133 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpo_r_z575/job_working_directory/000/3/outputs/galaxy_dataset_89d82b28-b154-4b39-9e19-48b26e4e974f.dat to /tmp/tmpo_r_z575/files/8/9/d/dataset_89d82b28-b154-4b39-9e19-48b26e4e974f.dat\n-\n-galaxy.model.metadata DEBUG 2023-04-14 08:59:50,280 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.model.metadata DEBUG 2023-04-14 08:59:50,300 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 4\n-galaxy.model.metadata DEBUG 2023-04-14 08:59:50,317 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 5\n-galaxy.jobs DEBUG 2023-04-14 08:59:50,491 [pN:main.1,p:60848,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (377.147 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_remove_chimera (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/log_cluster_filter.txt --- a/test-data/log_cluster_filter.txt Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,4407 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpt04nlgwt/galaxy-dev\n-Clonage dans \'/tmp/tmpt04nlgwt/galaxy-dev\'...\n-fait.\n-Mise \xc3\xa0 jour des fichiers: 87% (5412/6175)\rMise \xc3\xa0 jour des fichiers: 88% (5434/6175)\rMise \xc3\xa0 jour des fichiers: 89% (5496/6175)\rMise \xc3\xa0 jour des fichiers: 90% (5558/6175)\rMise \xc3\xa0 jour des fichiers: 91% (5620/6175)\rMise \xc3\xa0 jour des fichiers: 92% (5681/6175)\rMise \xc3\xa0 jour des fichiers: 93% (5743/6175)\rMise \xc3\xa0 jour des fichiers: 94% (5805/6175)\rMise \xc3\xa0 jour des fichiers: 95% (5867/6175)\rMise \xc3\xa0 jour des fichiers: 96% (5928/6175)\rMise \xc3\xa0 jour des fichiers: 97% (5990/6175)\rMise \xc3\xa0 jour des fichiers: 98% (6052/6175)\rMise \xc3\xa0 jour des fichiers: 99% (6114/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175), fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.0.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already s'..b'-unknown --offline --prefix /tmp/tmp0e0byafl/deps/_cache/7aceb47c --file /tmp/tmp0e0byafl/tmp/jobdepsi9acpvk650a80fe6225de7a3ec39e762f65eff821399f3b512517273aa2912df4da17ac1/__blast@2.10\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-24 12:41:23,375 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] Executing command: /home/vdarbot/miniconda3/bin/conda clean --tarballs -y\n-galaxy.jobs.runners ERROR 2023-04-24 12:41:23,872 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] (4) Failure preparing job\n-Traceback (most recent call last):\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 262, in prepare_job\n- job_wrapper.runner_command_line = self.build_command_line(\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 301, in build_command_line\n- return build_command(\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 81, in build_command\n- __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n- if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n- self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n- return self.app.toolbox.dependency_manager.dependency_shell_commands(\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n- self.build_cache(requirements, **kwds)\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n- self.build_environment()\n- File "/tmp/tmp0e0byafl/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n- raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n-galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n-galaxy.jobs DEBUG 2023-04-24 12:41:23,881 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp0e0byafl/job_working_directory/000/4/outputs/galaxy_dataset_97aceb5f-017c-4369-ba43-dc82c1c7e195.dat to /tmp/tmp0e0byafl/files/9/7/a/dataset_97aceb5f-017c-4369-ba43-dc82c1c7e195.dat\n-galaxy.jobs DEBUG 2023-04-24 12:41:23,881 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp0e0byafl/job_working_directory/000/4/outputs/galaxy_dataset_02f9b27d-ebb1-4278-b358-f3d9b48741ed.dat to /tmp/tmp0e0byafl/files/0/2/f/dataset_02f9b27d-ebb1-4278-b358-f3d9b48741ed.dat\n-galaxy.jobs DEBUG 2023-04-24 12:41:23,881 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp0e0byafl/job_working_directory/000/4/outputs/galaxy_dataset_5313f1d9-9886-4cc9-92eb-867a98549f44.dat to /tmp/tmp0e0byafl/files/5/3/1/dataset_5313f1d9-9886-4cc9-92eb-867a98549f44.dat\n-galaxy.jobs DEBUG 2023-04-24 12:41:23,881 [pN:main.1,p:95856,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp0e0byafl/job_working_directory/000/4/outputs/galaxy_dataset_44eb313c-90b3-4a63-bc8c-cb0ebd3cafd8.dat to /tmp/tmp0e0byafl/files/4/4/e/dataset_44eb313c-90b3-4a63-bc8c-cb0ebd3cafd8.dat\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_cluster_filters (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/log_clustering.txt --- a/test-data/log_clustering.txt Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,3398 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpte1clwq8/galaxy-dev\n-Clonage dans \'/tmp/tmpte1clwq8/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.0.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'4603-8a03-9f6d64d86a2d.dat\' --distance 1 --fastidious]\n-galaxy.jobs.runners DEBUG 2023-04-14 08:50:10,389 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] (6) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpcq21inwm/job_working_directory/000/6/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpcq21inwm/job_working_directory/000/6/galaxy_6.ec; \n-if [ -f "/tmp/tmpcq21inwm/job_working_directory/000/6/working/seeds.fasta" ] ; then cp "/tmp/tmpcq21inwm/job_working_directory/000/6/working/seeds.fasta" "/tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_14ba7874-54ce-43a5-87a6-b7a1c47d6283.dat" ; fi; \n-if [ -f "/tmp/tmpcq21inwm/job_working_directory/000/6/working/abundance.biom" ] ; then cp "/tmp/tmpcq21inwm/job_working_directory/000/6/working/abundance.biom" "/tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_3096e670-1508-4844-87c0-41e9f0aa6534.dat" ; fi; \n-if [ -f "/tmp/tmpcq21inwm/job_working_directory/000/6/working/swarms.tsv" ] ; then cp "/tmp/tmpcq21inwm/job_working_directory/000/6/working/swarms.tsv" "/tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_257d6537-09d0-4603-8a03-9f6d64d86a2d.dat" ; fi; cd \'/tmp/tmpcq21inwm/job_working_directory/000/6\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-14 08:50:10,406 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] (6) executing job script: /tmp/tmpcq21inwm/job_working_directory/000/6/galaxy_6.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-14 08:50:51,797 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 60087\n-galaxy.jobs.runners.local DEBUG 2023-04-14 08:50:51,798 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmpcq21inwm/job_working_directory/000/6/galaxy_6.sh\n-galaxy.jobs DEBUG 2023-04-14 08:50:51,850 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_14ba7874-54ce-43a5-87a6-b7a1c47d6283.dat to /tmp/tmpcq21inwm/files/1/4/b/dataset_14ba7874-54ce-43a5-87a6-b7a1c47d6283.dat\n-galaxy.jobs DEBUG 2023-04-14 08:50:51,850 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_3096e670-1508-4844-87c0-41e9f0aa6534.dat to /tmp/tmpcq21inwm/files/3/0/9/dataset_3096e670-1508-4844-87c0-41e9f0aa6534.dat\n-galaxy.jobs DEBUG 2023-04-14 08:50:51,850 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmpcq21inwm/job_working_directory/000/6/outputs/galaxy_dataset_257d6537-09d0-4603-8a03-9f6d64d86a2d.dat to /tmp/tmpcq21inwm/files/2/5/7/dataset_257d6537-09d0-4603-8a03-9f6d64d86a2d.dat\n-galaxy.model.metadata DEBUG 2023-04-14 08:50:51,887 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 8\n-galaxy.model.metadata DEBUG 2023-04-14 08:50:51,910 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 9\n-\n-galaxy.model.metadata DEBUG 2023-04-14 08:50:51,950 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 10\n-galaxy.jobs DEBUG 2023-04-14 08:50:52,161 [pN:main.1,p:58093,tN:LocalRunner.work_thread-3] job_wrapper.finish for job 6 executed (321.489 ms)\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 2 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_clustering (Test #1): failed\n-FROGS_clustering (Test #2): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/log_itsx.txt --- a/test-data/log_itsx.txt Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,2969 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpwwu6f1vn/galaxy-dev\n-Clonage dans \'/tmp/tmpwwu6f1vn/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.0.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b' defaults --unknown --offline --prefix /tmp/tmpd3p5ubjb/deps/_cache/9f25569a --file /tmp/tmpd3p5ubjb/tmp/jobdepsgq21duab6e7112901d5dd6e96453a8b7da7ce67279ca30759431991ef0a96736574ad7cc/__itsx@1.1.2\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-14 09:34:12,729 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] Executing command: /home/vdarbot/miniconda3/bin/conda clean --tarballs -y\n-galaxy.jobs.runners ERROR 2023-04-14 09:34:13,259 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] (3) Failure preparing job\n-Traceback (most recent call last):\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 262, in prepare_job\n- job_wrapper.runner_command_line = self.build_command_line(\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 301, in build_command_line\n- return build_command(\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 81, in build_command\n- __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n- if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n- self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n- return self.app.toolbox.dependency_manager.dependency_shell_commands(\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n- self.build_cache(requirements, **kwds)\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n- self.build_environment()\n- File "/tmp/tmpd3p5ubjb/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n- raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n-galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n-galaxy.jobs DEBUG 2023-04-14 09:34:13,270 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] fail(): Moved /tmp/tmpd3p5ubjb/job_working_directory/000/3/outputs/galaxy_dataset_eb210f71-b7d0-4eed-baab-fa570cba8b2b.dat to /tmp/tmpd3p5ubjb/files/e/b/2/dataset_eb210f71-b7d0-4eed-baab-fa570cba8b2b.dat\n-galaxy.jobs DEBUG 2023-04-14 09:34:13,271 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] fail(): Moved /tmp/tmpd3p5ubjb/job_working_directory/000/3/outputs/galaxy_dataset_d893a6fe-8b40-46f5-938e-7342b0c55609.dat to /tmp/tmpd3p5ubjb/files/d/8/9/dataset_d893a6fe-8b40-46f5-938e-7342b0c55609.dat\n-galaxy.jobs DEBUG 2023-04-14 09:34:13,271 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] fail(): Moved /tmp/tmpd3p5ubjb/job_working_directory/000/3/outputs/galaxy_dataset_6adbd5e6-23b2-454a-b3fe-00b90d1e5175.dat to /tmp/tmpd3p5ubjb/files/6/a/d/dataset_6adbd5e6-23b2-454a-b3fe-00b90d1e5175.dat\n-galaxy.jobs DEBUG 2023-04-14 09:34:13,271 [pN:main.1,p:70738,tN:LocalRunner.work_thread-1] fail(): Moved /tmp/tmpd3p5ubjb/job_working_directory/000/3/outputs/galaxy_dataset_711d0d72-2bfc-461c-825e-2f5d09ec28ed.dat to /tmp/tmpd3p5ubjb/files/7/1/1/dataset_711d0d72-2bfc-461c-825e-2f5d09ec28ed.dat\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_itsx (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/log_itsx_2.txt --- a/test-data/log_itsx_2.txt Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,2123 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmplk5ol3bv/galaxy-dev\n-Clonage dans \'/tmp/tmplk5ol3bv/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'utputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpdsj8fglo/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpdsj8fglo/job_working_directory/000/3/galaxy_3.ec; \n-if [ -f "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/out_removed.fasta" ] ; then cp "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/out_removed.fasta" "/tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_0b3c0f65-0f64-4b9d-bb19-88848296bee2.dat" ; fi; \n-if [ -f "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/itsx.fasta" ] ; then cp "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/itsx.fasta" "/tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_272b90f4-455c-4b37-acca-d2ba900832bf.dat" ; fi; \n-if [ -f "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/itsx.biom" ] ; then cp "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/itsx.biom" "/tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_785a7a4c-b2d5-472c-b215-60167be9b383.dat" ; fi; \n-if [ -f "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/report.html" ] ; then cp "/tmp/tmpdsj8fglo/job_working_directory/000/3/working/report.html" "/tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_f732cc6d-108e-4666-82ec-c76136a23aa5.dat" ; fi; cd \'/tmp/tmpdsj8fglo/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-24 12:30:42,301 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] (3) executing job script: /tmp/tmpdsj8fglo/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-24 12:30:51,283 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 94333\n-galaxy.jobs.runners.local DEBUG 2023-04-24 12:30:51,283 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpdsj8fglo/job_working_directory/000/3/galaxy_3.sh\n-galaxy.jobs DEBUG 2023-04-24 12:30:51,326 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_0b3c0f65-0f64-4b9d-bb19-88848296bee2.dat to /tmp/tmpdsj8fglo/files/0/b/3/dataset_0b3c0f65-0f64-4b9d-bb19-88848296bee2.dat\n-galaxy.jobs DEBUG 2023-04-24 12:30:51,327 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_272b90f4-455c-4b37-acca-d2ba900832bf.dat to /tmp/tmpdsj8fglo/files/2/7/2/dataset_272b90f4-455c-4b37-acca-d2ba900832bf.dat\n-galaxy.jobs DEBUG 2023-04-24 12:30:51,327 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_785a7a4c-b2d5-472c-b215-60167be9b383.dat to /tmp/tmpdsj8fglo/files/7/8/5/dataset_785a7a4c-b2d5-472c-b215-60167be9b383.dat\n-galaxy.jobs DEBUG 2023-04-24 12:30:51,327 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpdsj8fglo/job_working_directory/000/3/outputs/galaxy_dataset_f732cc6d-108e-4666-82ec-c76136a23aa5.dat to /tmp/tmpdsj8fglo/files/f/7/3/dataset_f732cc6d-108e-4666-82ec-c76136a23aa5.dat\n-galaxy.model.metadata DEBUG 2023-04-24 12:30:51,408 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.model.metadata DEBUG 2023-04-24 12:30:51,442 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 4\n-galaxy.model.metadata DEBUG 2023-04-24 12:30:51,451 [pN:main.1,p:94225,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 5\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_itsx (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/log_preprocess.txt --- a/test-data/log_preprocess.txt Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1951 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp9rmcpqjk/galaxy-dev\n-Clonage dans \'/tmp/tmp9rmcpqjk/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.0.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'hread] Calling on_field_end with no data\n-multipart.multipart DEBUG 2023-04-13 21:16:08,633 [pN:main.1,p:45312,tN:MainThread] Calling on_end with no data\n-\n-galaxy.tools INFO 2023-04-13 21:16:09,139 [pN:main.1,p:45312,tN:WSGI_0] Validated and populated state for tool request (16.082 ms)\n-galaxy.tools.actions.upload DEBUG 2023-04-13 21:16:09,148 [pN:main.1,p:45312,tN:WSGI_0] Persisted uploads (0.129 ms)\n-galaxy.tools.actions.upload DEBUG 2023-04-13 21:16:09,339 [pN:main.1,p:45312,tN:WSGI_0] Checked uploads (191.181 ms)\n-galaxy.tools.actions.upload DEBUG 2023-04-13 21:16:09,343 [pN:main.1,p:45312,tN:WSGI_0] Created upload job (3.659 ms)\n-galaxy.tools.execute DEBUG 2023-04-13 21:16:09,343 [pN:main.1,p:45312,tN:WSGI_0] Tool upload1 created job None (195.550 ms)\n-galaxy.web_stack.handlers INFO 2023-04-13 21:16:09,388 [pN:main.1,p:45312,tN:WSGI_0] (Job[id=2,tool_id=upload1]) Handler \'_default_\' assigned using \'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED\' assignment method\n-galaxy.tools.execute DEBUG 2023-04-13 21:16:09,416 [pN:main.1,p:45312,tN:WSGI_0] Created 1 job(s) for tool upload1 request (277.313 ms)\n-\n-galaxy.jobs.mapper DEBUG 2023-04-13 21:16:09,914 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: upload_dest\n-galaxy.jobs.handler DEBUG 2023-04-13 21:16:09,922 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to planemo_runner runner\n-galaxy.jobs DEBUG 2023-04-13 21:16:09,993 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: upload_dest)\n-galaxy.jobs DEBUG 2023-04-13 21:16:10,010 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /tmp/tmp9rmcpqjk/job_working_directory/000/2\n-galaxy.jobs.runners DEBUG 2023-04-13 21:16:10,044 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] Job [2] queued (121.464 ms)\n-galaxy.jobs.handler INFO 2023-04-13 21:16:10,060 [pN:main.1,p:45312,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n-galaxy.jobs DEBUG 2023-04-13 21:16:10,221 [pN:main.1,p:45312,tN:LocalRunner.work_thread-2] Job wrapper for Job [2] prepared (131.529 ms)\n-galaxy.jobs.command_factory INFO 2023-04-13 21:16:10,240 [pN:main.1,p:45312,tN:LocalRunner.work_thread-2] Built script [/tmp/tmp9rmcpqjk/job_working_directory/000/2/tool_script.sh] for tool command [python \'/tmp/tmp9rmcpqjk/galaxy-dev/tools/data_source/upload.py\' \'/tmp/tmp9rmcpqjk/galaxy-dev\' \'/tmp/tmp9rmcpqjk/job_working_directory/000/2/registry.xml\' \'/tmp/tmp9rmcpqjk/tmp/upload_params_smi_3ore\' \'2:/tmp/tmp9rmcpqjk/job_working_directory/000/2/working/dataset_1c6df421-4c92-4641-a2a3-3d1a72a61e9d_files:/tmp/tmp9rmcpqjk/job_working_directory/000/2/outputs/galaxy_dataset_1c6df421-4c92-4641-a2a3-3d1a72a61e9d.dat\']\n-galaxy.jobs.runners DEBUG 2023-04-13 21:16:10,303 [pN:main.1,p:45312,tN:LocalRunner.work_thread-2] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmp9rmcpqjk/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp9rmcpqjk/job_working_directory/000/2/galaxy_2.ec; cd \'/tmp/tmp9rmcpqjk/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-13 21:16:10,320 [pN:main.1,p:45312,tN:LocalRunner.work_thread-2] (2) executing job script: /tmp/tmp9rmcpqjk/job_working_directory/000/2/galaxy_2.sh\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 2 test(s) - out of 2 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_preprocess (Test #1): failed\n-FROGS_preprocess (Test #2): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/multihits.tsv --- a/test-data/multihits.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,865 +0,0 @@\n-#observation_name\tblast_taxonomy\t blast_subject\tblast_perc_identity\tblast_perc_query_coverage\tblast_evalue\tblast_aln_length\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tLXJJ02000010.3161.4631\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli S88\tCU928161.4443202.4444743\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCU651637.2709763.2711303\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli O157:H7\tCP033605.4932246.4933797\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Shigella flexneri\tCP033510.2312050.2313603\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli O32:H37 str. P4\tAJQW01000057.1.1280\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP032515.4680373.4681924\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP032265.2506313.2507866\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli DEC8C\tAIGH01000069.160053.161583\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;unknown species\tJX984110.1.1220\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCU651637.3470321.3471862\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli O157:H7\tCP033605.5076505.5078058\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Shigella flexneri\tCP033510.2451439.2452992\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP031134.1449423.1450976\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP030919.3931874.3933427\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia albertii\tCP030783.4472057.4473578\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli S88\tCU928161.4403031.4404573\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli 55989\tCU928145.3776861.3778402\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCU651637.227496.229042\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP032515.4721466.4723017\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli\tCP032265.3415857.3417410\t100.0\t100.0\t0.0\t426\n-Cluster_2\tBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli O157:H7\tCP033605.4835899.4837452'..b'bacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tAL111168.39249.40761\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tAL111168.696424.697936\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tZ29326.264.1776\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tCP013116.654878.656395\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tCP013116.351319.352836\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tJX912519.1.1435\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tCP013034.1173635.1175152\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tCP013034.894477.895994\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tCP013034.1570901.1572418\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter jejuni\tAF550626.1.1417\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tAF550622.1.1417\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tAF550621.1.1417\t100.0\t100.0\t0.0\t402\n-Cluster_7\tBacteria;Campylobacterota;Campylobacteria;Campylobacterales;Campylobacteraceae;Campylobacter;Campylobacter coli\tAF550620.1.1417\t100.0\t100.0\t0.0\t402\n-Cluster_10\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;unknown genus;Clostridium sp.\tGU128175.1.1435\t99.5\t100.0\t0.0\t404\n-Cluster_10\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;unknown genus;Clostridium sp.\tJN874874.1.1444\t99.5\t100.0\t0.0\t404\n-Cluster_11\tBacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species\tEF025229.1.1453\t99.75\t100.0\t0.0\t401\n-Cluster_11\tBacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species\tGQ175509.1.1455\t99.75\t100.0\t0.0\t401\n-Cluster_11\tBacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species\tFJ440057.1.1453\t99.75\t100.0\t0.0\t401\n-Cluster_11\tBacteria;Firmicutes;Clostridia;Lachnospirales;Lachnospiraceae;[Ruminococcus] torques group;unknown species\tJQ248111.1.1514\t99.75\t100.0\t0.0\t401\n-Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;unknown species\tEU763264.1.1364\t100.0\t100.0\t0.0\t404\n-Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;unknown species\tEU767001.1.1361\t100.0\t100.0\t0.0\t404\n-Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;unknown species\tEU767866.1.1364\t100.0\t100.0\t0.0\t404\n-Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;unknown species\tEU767539.1.1358\t100.0\t100.0\t0.0\t404\n-Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Flavonifractor plautii\tCP015406.84360.85899\t100.0\t100.0\t0.0\t404\n-Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Flavonifractor plautii\tAY724678.1.1465\t100.0\t100.0\t0.0\t404\n-Cluster_12\tBacteria;Firmicutes;Clostridia;Oscillospirales;Oscillospiraceae;Flavonifractor;Flavonifractor plautii\tY18187.1.1550\t100.0\t100.0\t0.0\t404\n' |
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diff -r b2967b704d6b -r f479218f3736 test-data/phyloseq_alpha_diversity.nb.html --- a/test-data/phyloseq_alpha_diversity.nb.html Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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diff -r b2967b704d6b -r f479218f3736 test-data/phyloseq_alpha_diversity.tsv --- a/test-data/phyloseq_alpha_diversity.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,65 +0,0 @@ - Observed Chao1 se.chao1 Shannon -DLT0.LOT08 210 210 0 2.01603767724795 -DLT0.LOT05 221 254.785714285714 13.3895041926063 1.79800937304124 -DLT0.LOT03 226 226 0 3.45528429286049 -DLT0.LOT07 221 221 0 2.98216090690738 -DLT0.LOT06 278 278 0 3.20952140178085 -DLT0.LOT01 281 281 0 4.10685205650844 -DLT0.LOT04 247 247 0 2.47304361554073 -DLT0.LOT10 236 236 0 3.55173827807196 -MVT0.LOT05 158 158 0 2.34503849832531 -MVT0.LOT01 128 128 0 2.28541492757583 -MVT0.LOT06 157 157 0 3.92479836105885 -MVT0.LOT07 157 157 0 3.75898496293381 -MVT0.LOT03 160 160 0 3.34027078029461 -MVT0.LOT09 122 122 0 3.95221379962838 -MVT0.LOT08 124 124 0 2.30012425431142 -MVT0.LOT10 95 95 0 1.25959560361526 -BHT0.LOT01 103 103 0 2.53131370126125 -BHT0.LOT07 144 144 0 3.15166550279444 -BHT0.LOT06 155 155 0 2.92765820448176 -BHT0.LOT03 153 153 0 2.95001637842565 -BHT0.LOT10 159 159 0 2.7790079222459 -BHT0.LOT05 183 183 0 2.53671816912042 -BHT0.LOT04 209 209 0 3.47635995384084 -BHT0.LOT08 178 178 0 3.09192502544742 -VHT0.LOT02 132 132 0 1.4154609826759 -VHT0.LOT10 134 134 0 1.87555746873306 -VHT0.LOT03 206 206 0 3.51078572003616 -VHT0.LOT01 235 235 0 2.67402666784541 -VHT0.LOT08 157 157 0 3.31989163716182 -VHT0.LOT06 182 182 0 1.88583439498533 -VHT0.LOT07 156 156 0 1.41904291231118 -VHT0.LOT04 193 193 0 2.64373071960283 -SFT0.LOT08 111 165.473684210526 21.5900554349517 1.13874307530455 -SFT0.LOT07 110 110 0 2.96744303252776 -SFT0.LOT06 126 126 0 2.49355558700118 -SFT0.LOT03 119 119 0 2.92356922933234 -SFT0.LOT02 104 104 0 2.47818417340797 -SFT0.LOT05 75 210.125 60.9771168818602 1.33504649810823 -SFT0.LOT04 70 70 0 1.4778600596069 -SFT0.LOT01 117 117 0 1.98786858579725 -FST0.LOT07 150 150 0 2.99751683958306 -FST0.LOT08 152 152 0 3.4863921810005 -FST0.LOT05 156 156 0 3.37246744717753 -FST0.LOT06 165 165 0 3.40841441699795 -FST0.LOT01 149 149 0 2.43179269800015 -FST0.LOT03 168 168 0 2.92905427377967 -FST0.LOT10 186 186 0 3.03616027233611 -FST0.LOT02 179 179 0 3.18742279060019 -FCT0.LOT06 140 140 0 3.08227430433618 -FCT0.LOT10 172 172 0 3.89564247946871 -FCT0.LOT05 166 166 0 1.99860208269453 -FCT0.LOT03 197 197 0 2.70414675332528 -FCT0.LOT08 218 218 0 3.88853679266027 -FCT0.LOT02 195 195 0 2.55307056135657 -FCT0.LOT07 199 199 0 3.50534515553006 -FCT0.LOT01 200 200 0 3.88749477420522 -CDT0.LOT10 125 125 0 1.04948460066206 -CDT0.LOT08 175 175 0 3.25853898017873 -CDT0.LOT05 264 264 0 4.2074225334087 -CDT0.LOT04 269 269 0 4.45683686305649 -CDT0.LOT06 119 119 0 1.23721179294724 -CDT0.LOT09 177 177 0 1.91666097264414 -CDT0.LOT07 161 161 0 3.09013417675057 -CDT0.LOT02 174 174 0 2.42745280040353 |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/phyloseq_beta --- a/test-data/phyloseq_beta Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1019 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp0r1_03t5/galaxy-dev\n-Clonage dans \'/tmp/tmp0r1_03t5/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b' > \'/tmp/tmp0r1_03t5/tmp/jobdeps4kqb1j_rae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0\'\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-05-04 11:01:15,333 [pN:main.1,p:148137,tN:LocalRunner.work_thread-0] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --strict-channel-priority --override-channels --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmp0r1_03t5/deps/_cache/49469f18 --file /tmp/tmp0r1_03t5/tmp/jobdeps4kqb1j_rae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-05-04 11:01:48,691 [pN:main.1,p:148137,tN:LocalRunner.work_thread-0] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmp0r1_03t5/deps/_cache/49469f18 --file /tmp/tmp0r1_03t5/tmp/jobdeps4kqb1j_rae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-05-04 11:02:00,522 [pN:main.1,p:148137,tN:LocalRunner.work_thread-0] Executing command: /home/vdarbot/miniconda3/bin/conda clean --tarballs -y\n-galaxy.jobs.runners ERROR 2023-05-04 11:02:01,265 [pN:main.1,p:148137,tN:LocalRunner.work_thread-0] (2) Failure preparing job\n-Traceback (most recent call last):\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 262, in prepare_job\n- job_wrapper.runner_command_line = self.build_command_line(\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 301, in build_command_line\n- return build_command(\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 81, in build_command\n- __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n- if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n- self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n- return self.app.toolbox.dependency_manager.dependency_shell_commands(\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n- self.build_cache(requirements, **kwds)\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n- self.build_environment()\n- File "/tmp/tmp0r1_03t5/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n- raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n-galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n-galaxy.jobs DEBUG 2023-05-04 11:02:01,293 [pN:main.1,p:148137,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp0r1_03t5/job_working_directory/000/2/outputs/galaxy_dataset_65844486-b9e0-448d-a4e7-c957aa6072f2.dat to /tmp/tmp0r1_03t5/files/6/5/8/dataset_65844486-b9e0-448d-a4e7-c957aa6072f2.dat\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGSSTAT_Phyloseq_Beta_Diversity (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/phyloseq_beta.log --- a/test-data/phyloseq_beta.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1933 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpad8ioi4m/galaxy-dev\n-Clonage dans \'/tmp/tmpad8ioi4m/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'q $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-9dee567f8c5699ef583dd7c0b3a5ebc0a1f72d2a74b08bf3a782619c50641ad7\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-9dee567f8c5699ef583dd7c0b3a5ebc0a1f72d2a74b08bf3a782619c50641ad7\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-9dee567f8c5699ef583dd7c0b3a5ebc0a1f72d2a74b08bf3a782619c50641ad7\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-9dee567f8c5699ef583dd7c0b3a5ebc0a1f72d2a74b08bf3a782619c50641ad7\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; phyloseq_beta_diversity.py --rdata \'/tmp/tmpad8ioi4m/files/7/7/d/dataset_77d86ccc-5832-4281-891a-9cc9d46b5a13.dat\' --varExp \'EnvType\' --distance-methods \'cc,unifrac\' --matrix-outdir \'BetaMatrix\' --html \'/tmp/tmpad8ioi4m/job_working_directory/000/2/outputs/galaxy_dataset_988dd726-32cd-49ca-95ac-0092e604cda6.dat\']\n-galaxy.jobs.runners DEBUG 2023-05-09 09:01:51,694 [pN:main.1,p:21421,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpad8ioi4m/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpad8ioi4m/job_working_directory/000/2/galaxy_2.ec; \n-if [ -f "/tmp/tmpad8ioi4m/job_working_directory/000/2/working/beta_diversity.nb.html" ] ; then cp "/tmp/tmpad8ioi4m/job_working_directory/000/2/working/beta_diversity.nb.html" "/tmp/tmpad8ioi4m/job_working_directory/000/2/outputs/galaxy_dataset_988dd726-32cd-49ca-95ac-0092e604cda6.dat" ; fi; cd \'/tmp/tmpad8ioi4m/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-09 09:01:51,720 [pN:main.1,p:21421,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmpad8ioi4m/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 09:02:22,742 [pN:main.1,p:21421,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 31392\n-galaxy.jobs.runners.local DEBUG 2023-05-09 09:02:22,745 [pN:main.1,p:21421,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmpad8ioi4m/job_working_directory/000/2/galaxy_2.sh\n-galaxy.jobs DEBUG 2023-05-09 09:02:22,864 [pN:main.1,p:21421,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpad8ioi4m/job_working_directory/000/2/outputs/galaxy_dataset_988dd726-32cd-49ca-95ac-0092e604cda6.dat to /tmp/tmpad8ioi4m/files/9/8/8/dataset_988dd726-32cd-49ca-95ac-0092e604cda6.dat\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGSSTAT_Phyloseq_Beta_Diversity (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/phyloseq_import.log --- a/test-data/phyloseq_import.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,4772 +0,0 @@\n-Traceback (most recent call last):\n- File "/home/vdarbot/.local/bin/planemo", line 5, in <module>\n- from planemo.cli import planemo\n-ModuleNotFoundError: No module named \'planemo\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpf4wcyew3/galaxy-dev\n-Clonage dans \'/tmp/tmpf4wcyew3/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: ale'..b'? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; phyloseq_import_data.py --biomfile \'/tmp/tmpxabawrwn/files/4/3/4/dataset_434a7334-afaf-49b1-ba0f-31e716f2d862.dat\' --samplefile \'/tmp/tmpxabawrwn/files/2/1/c/dataset_21ca4a43-514c-4a2f-bb48-192e0d7f8eae.dat\' --treefile \'/tmp/tmpxabawrwn/files/a/3/b/dataset_a3bbbfdb-4632-46c5-b438-98b059b1dae2.dat\' --ranks Kingdom Phylum Class Order Family Genus Species --html \'/tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_50731ca5-13e1-4fed-9fbc-202ba6a8e124.dat\' --rdata \'/tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_316c9e1c-9c8f-4b9e-93d3-9154ca0b0020.dat\']\n-galaxy.jobs.runners DEBUG 2023-05-04 10:48:35,016 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] (4) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpxabawrwn/job_working_directory/000/4/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpxabawrwn/job_working_directory/000/4/galaxy_4.ec; \n-if [ -f "/tmp/tmpxabawrwn/job_working_directory/000/4/working/asv_data.Rdata" ] ; then cp "/tmp/tmpxabawrwn/job_working_directory/000/4/working/asv_data.Rdata" "/tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_316c9e1c-9c8f-4b9e-93d3-9154ca0b0020.dat" ; fi; \n-if [ -f "/tmp/tmpxabawrwn/job_working_directory/000/4/working/report.nb.html" ] ; then cp "/tmp/tmpxabawrwn/job_working_directory/000/4/working/report.nb.html" "/tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_50731ca5-13e1-4fed-9fbc-202ba6a8e124.dat" ; fi; cd \'/tmp/tmpxabawrwn/job_working_directory/000/4\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-04 10:48:35,034 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] (4) executing job script: /tmp/tmpxabawrwn/job_working_directory/000/4/galaxy_4.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-04 10:48:49,807 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 147064\n-galaxy.jobs.runners.local DEBUG 2023-05-04 10:48:49,807 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmpxabawrwn/job_working_directory/000/4/galaxy_4.sh\n-galaxy.jobs DEBUG 2023-05-04 10:48:49,866 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_316c9e1c-9c8f-4b9e-93d3-9154ca0b0020.dat to /tmp/tmpxabawrwn/files/3/1/6/dataset_316c9e1c-9c8f-4b9e-93d3-9154ca0b0020.dat\n-galaxy.jobs DEBUG 2023-05-04 10:48:49,866 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmpxabawrwn/job_working_directory/000/4/outputs/galaxy_dataset_50731ca5-13e1-4fed-9fbc-202ba6a8e124.dat to /tmp/tmpxabawrwn/files/5/0/7/dataset_50731ca5-13e1-4fed-9fbc-202ba6a8e124.dat\n-galaxy.model.metadata DEBUG 2023-05-04 10:48:49,894 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 4\n-galaxy.model.metadata DEBUG 2023-05-04 10:48:49,902 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 5\n-galaxy.jobs DEBUG 2023-05-04 10:48:49,998 [pN:main.1,p:146938,tN:LocalRunner.work_thread-3] job_wrapper.finish for job 4 executed (138.053 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGSSTAT_Phyloseq_Import_Data (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/phyloseq_manova.html --- a/test-data/phyloseq_manova.html Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1943 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpcmrjfx4c/galaxy-dev\n-Clonage dans \'/tmp/tmpcmrjfx4c/galaxy-dev\'...\n-fait.\n-Mise \xc3\xa0 jour des fichiers: 96% (5977/6175)\rMise \xc3\xa0 jour des fichiers: 97% (5990/6175)\rMise \xc3\xa0 jour des fichiers: 98% (6052/6175)\rMise \xc3\xa0 jour des fichiers: 99% (6114/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175), fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-p'..b'd15031\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-dbbdef0a126c47fedd769f0626029b80e8d70048c298b953c5df12ebc3d15031\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-dbbdef0a126c47fedd769f0626029b80e8d70048c298b953c5df12ebc3d15031\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-dbbdef0a126c47fedd769f0626029b80e8d70048c298b953c5df12ebc3d15031\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; phyloseq_manova.py --rdata \'/tmp/tmpcmrjfx4c/files/e/b/9/dataset_eb9da6fd-a90e-43f2-97f0-6ae9c961e49d.dat\' --varExp \'EnvType\' --distance-matrix \'/tmp/tmpcmrjfx4c/files/e/2/4/dataset_e249ce0e-97c6-4f34-a568-0e388a7121c8.dat\' --html \'/tmp/tmpcmrjfx4c/job_working_directory/000/3/outputs/galaxy_dataset_022f0c6b-6cec-45d2-aae8-251561944899.dat\']\n-galaxy.jobs.runners DEBUG 2023-05-04 11:02:16,249 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] (3) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpcmrjfx4c/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpcmrjfx4c/job_working_directory/000/3/galaxy_3.ec; \n-if [ -f "/tmp/tmpcmrjfx4c/job_working_directory/000/3/working/manova.nb.html" ] ; then cp "/tmp/tmpcmrjfx4c/job_working_directory/000/3/working/manova.nb.html" "/tmp/tmpcmrjfx4c/job_working_directory/000/3/outputs/galaxy_dataset_022f0c6b-6cec-45d2-aae8-251561944899.dat" ; fi; cd \'/tmp/tmpcmrjfx4c/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-04 11:02:16,263 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] (3) executing job script: /tmp/tmpcmrjfx4c/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-04 11:02:33,355 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 178722\n-galaxy.jobs.runners.local DEBUG 2023-05-04 11:02:33,355 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmpcmrjfx4c/job_working_directory/000/3/galaxy_3.sh\n-galaxy.jobs DEBUG 2023-05-04 11:02:33,388 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpcmrjfx4c/job_working_directory/000/3/outputs/galaxy_dataset_022f0c6b-6cec-45d2-aae8-251561944899.dat to /tmp/tmpcmrjfx4c/files/0/2/2/dataset_022f0c6b-6cec-45d2-aae8-251561944899.dat\n-galaxy.model.metadata DEBUG 2023-05-04 11:02:33,456 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.jobs DEBUG 2023-05-04 11:02:33,558 [pN:main.1,p:178626,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (176.376 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/phyloseq_manova.nb.html --- a/test-data/phyloseq_manova.nb.html Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1910 +0,0 @@\n-<!DOCTYPE html>\n-\n-<html>\n-\n-<head>\n-\n-<meta charset="utf-8" />\n-<meta name="generator" content="pandoc" />\n-<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />\n-\n-\n-\n-\n-<title>FROGS Phyloseq: Multivariate Analysis of Variance (version 4.1.0)</title>\n-\n-<script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to\n-// be compatible with the behavior of Pandoc < 2.8).\n-document.addEventListener(\'DOMContentLoaded\', function(e) {\n- var hs = document.querySelectorAll("div.section[class*=\'level\'] > :first-child");\n- var i, h, a;\n- for (i = 0; i < hs.length; i++) {\n- h = hs[i];\n- if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6\n- a = h.attributes;\n- while (a.length > 0) h.removeAttribute(a[0].name);\n- }\n-});\n-</script>\n-<script>/*! jQuery v3.6.0 | (c) OpenJS Foundation and other contributors | jquery.org/license */\n-!function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undefined"!=typeof window?window:this,function(C,e){"use strict";var t=[],r=Object.getPrototypeOf,s=t.slice,g=t.flat?function(e){return t.flat.call(e)}:function(e){return 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() {\n- window.initializeSourceEmbed("phyloseq_manova.Rmd");\n- window.initializeCodeFolding("hide" === "show");\n-});\n-</script>\n-\n-\n-<!-- dynamically load mathjax for compatibility with self-contained -->\n-<script>\n- (function () {\n- var script = document.createElement("script");\n- script.type = "text/javascript";\n- script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";\n- document.getElementsByTagName("head")[0].appendChild(script);\n- })();\n-</script>\n-\n-</body>\n-</html>\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test.log --- a/test-data/planemo_test.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,18230 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpjctq_t9e/galaxy-dev\n-Clonage dans \'/tmp/tmpjctq_t9e/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vd'..b'py", line 1900, in _execute_context\n- self.dialect.do_execute(\n- File "/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 736, in do_execute\n- cursor.execute(statement, parameters)\n-sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked\n-[SQL: SELECT job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id \n-FROM history_dataset_collection_association, job_to_output_dataset_collection \n-WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.metadata, history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata_deferred, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id \n-FROM history_dataset_association, job_to_output_dataset \n-WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 \n-FROM job \n-WHERE job.state IN (?, ?, ?) AND job.handler = ?]\n-[parameters: (<states.DELETED_NEW: \'deleted_new\'>, <states.DELETING: \'deleting\'>, <states.STOPPING: \'stop\'>, \'main.1\')]\n-(Background on this error at: https://sqlalche.me/e/14/e3q8)\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 7 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_affiliation_filters (Test #1): passed\n-FROGS_affiliation_filters (Test #2): passed\n-FROGS_affiliation_postprocess (Test #1): passed\n-FROGS_affiliation_stats (Test #1): passed\n-FROGS_biom_to_stdBiom (Test #1): passed\n-FROGS_biom_to_tsv (Test #1): passed\n-FROGS_cluster_filters (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test.sh --- a/test-data/planemo_test.sh Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,42 +0,0 @@ -#!/bin/sh -WRAPPER_DIR=~/Bureau/FROGS-wrappers/tools/frogs/ -DIR=planemo_test_4.1.0_vincentdarbot/ -mkdir -p $DIR - -# cd -# . planemo/bin/activate -# cd ~/Bureau/FROGS-wrappers/tools/frogs/test-data - -####################################################################################################### -# TEST LA STRUCTURE -for i in $WRAPPER_DIR/*.xml -do - echo $i - planemo lint $i > $DIR/`basename $i |sed 's/\.xml//'`.lint.log 2>&1 -done - -grep Failed $DIR/*.lint.log - -####################################################################################################### -# VALIDE L'EXECUTION -for i in `ls $WRAPPER_DIR/*.xml | grep -v frogsfunc` -do - echo $i - planemo test --no_cleanup --conda_channels vincentdarbot,conda-forge,bioconda,defaults $i > $DIR/$(basename $i | sed 's/\.xml//').test.log 2>&1 -done - -# si erreur sur github action alors tester -# planemo test --no_cleanup --docker $i > ~/workspace/toolshed_doc/planemo_test_3.2.3_galaxy3/$(basename $i | sed 's/\.xml//').dockertest.log 2>&1 - -grep FAILED $DIR/*test.log - - -grep "test(s) executed passed" $DIR/*test.log - -####################################################################################################### -# TEST SOUS GALAXY - -####################################################################################################### -# SOUMISSION AU TOOLSHED - - |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_2.log --- a/test-data/planemo_test_2.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,3399 +0,0 @@\n-planemo couldn\'t find a target test-data directory, you should likely create a test-data directory or pass an explicit path using --test_data.\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpm9gahpt0/galaxy-dev\n-Clonage dans \'/tmp/tmpm9gahpt0/galaxy-dev\'...\n-fait.\n-Mise \xc3\xa0 jour des fichiers: 81% (5022/6175)\rMise \xc3\xa0 jour des fichiers: 82% (5064/6175)\rMise \xc3\xa0 jour des fichiers: 83% (5126/6175)\rMise \xc3\xa0 jour des fichiers: 84% (5187/6175)\rMise \xc3\xa0 jour des fichiers: 85% (5249/6175)\rMise \xc3\xa0 jour des fichiers: 86% (5311/6175)\rMise \xc3\xa0 jour des fichiers: 87% (5373/6175)\rMise \xc3\xa0 jour des fichiers: 88% (5434/6175)\rMise \xc3\xa0 jour des fichiers: 89% (5496/6175)\rMise \xc3\xa0 jour des fichiers: 90% (5558/6175)\rMise \xc3\xa0 jour des fichiers: 91% (5620/6175)\rMise \xc3\xa0 jour des fichiers: 92% (5681/6175)\rMise \xc3\xa0 jour des fichiers: 93% (5743/6175)\rMise \xc3\xa0 jour des fichiers: 94% (5805/6175)\rMise \xc3\xa0 jour des fichiers: 95% (5867/6175)\rMise \xc3\xa0 jour des fichiers: 96% (5928/6175)\rMise \xc3\xa0 jour des fichiers: 97% (5990/6175)\rMise \xc3\xa0 jour des fichiers: 98% (6052/6175)\rMise \xc3\xa0 jour des fichiers: 99% (6114/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175), fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and p'..b'r(\n-bioblend.ConnectionError: Unexpected HTTP status code: 500: {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0, "traceback": "Traceback (most recent call last):\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 1900, in _execute_context\\n self.dialect.do_execute(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/default.py\\", line 736, in do_execute\\n cursor.execute(statement, parameters)\\nsqlite3.OperationalError: database is locked\\n\\nThe above exception was the direct cause of the following exception:\\n\\nTraceback (most recent call last):\\n File \\"/tmp/tmpt2afa7q5/galaxy-dev/lib/galaxy/web/framework/decorators.py\\", line 337, in decorator\\n rval = func(self, trans, *args, **kwargs)\\n File \\"/tmp/tmpt2afa7q5/galaxy-dev/lib/galaxy/webapps/galaxy/api/users.py\\", line 325, in create\\n user = trans.get_or_create_remote_user(remote_user_email=payload[\\"remote_user_email\\"])\\n File \\"/tmp/tmpt2afa7q5/galaxy-dev/lib/galaxy/webapps/base/webapp.py\\", line 740, in get_or_create_remote_user\\n self.sa_session.query(self.app.model.User)\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 2824, in first\\n return self.limit(1)._iter().first()\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 2916, in _iter\\n result = self.session.execute(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/orm/session.py\\", line 1714, in execute\\n result = conn._execute_20(statement, params or {}, execution_options)\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 1705, in _execute_20\\n return meth(self, args_10style, kwargs_10style, execution_options)\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/sql/elements.py\\", line 334, in _execute_on_connection\\n return connection._execute_clauseelement(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 1572, in _execute_clauseelement\\n ret = self._execute_context(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 1943, in _execute_context\\n self._handle_dbapi_exception(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 2124, in _handle_dbapi_exception\\n util.raise_(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/util/compat.py\\", line 211, in raise_\\n raise exception\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/base.py\\", line 1900, in _execute_context\\n self.dialect.do_execute(\\n File \\"/home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages/sqlalchemy/engine/default.py\\", line 736, in do_execute\\n cursor.execute(statement, parameters)\\nsqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked\\n[SQL: SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.username AS galaxy_user_username, galaxy_user.password AS galaxy_user_password, galaxy_user.last_password_change AS galaxy_user_last_password_change, galaxy_user.external AS galaxy_user_external, galaxy_user.form_values_id AS galaxy_user_form_values_id, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged, galaxy_user.disk_usage AS galaxy_user_disk_usage, galaxy_user.active AS galaxy_user_active, galaxy_user.activation_token AS galaxy_user_activation_token \\nFROM galaxy_user \\nWHERE galaxy_user.email = ?\\n LIMIT ? OFFSET ?]\\n[parameters: (\'planemo@galaxyproject.org\', 1, 0)]\\n(Background on this error at: https://sqlalche.me/e/14/e3q8)\\n"}\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_3.log --- a/test-data/planemo_test_3.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,17850 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp1lnw8o38/galaxy-dev\n-Clonage dans \'/tmp/tmp1lnw8o38/galaxy-dev\'...\n-fait.\n-Mise \xc3\xa0 jour des fichiers: 44% (2755/6175)\rMise \xc3\xa0 jour des fichiers: 45% (2779/6175)\rMise \xc3\xa0 jour des fichiers: 46% (2841/6175)\rMise \xc3\xa0 jour des fichiers: 47% (2903/6175)\rMise \xc3\xa0 jour des fichiers: 48% (2964/6175)\rMise \xc3\xa0 jour des fichiers: 49% (3026/6175)\rMise \xc3\xa0 jour des fichiers: 50% (3088/6175)\rMise \xc3\xa0 jour des fichiers: 51% (3150/6175)\rMise \xc3\xa0 jour des fichiers: 52% (3211/6175)\rMise \xc3\xa0 jour des fichiers: 53% (3273/6175)\rMise \xc3\xa0 jour des fichiers: 54% (3335/6175)\rMise \xc3\xa0 jour des fichiers: 55% (3397/6175)\rMise \xc3\xa0 jour des fichiers: 56% (3458/6175)\rMise \xc3\xa0 jour des fichiers: 57% (3520/6175)\rMise \xc3\xa0 jour des fichiers: 58% (3582/6175)\rMise \xc3\xa0 jour des fichiers: 59% (3644/6175)\rMise \xc3\xa0 jour des fichiers: 60% (3705/6175)\rMise \xc3\xa0 jour des fichiers: 61% (3767/6175)\rMise \xc3\xa0 jour des fichiers: 62% (3829/6175)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6175)\rMise \xc3\xa0 jour des fichiers: 64% (3952/6175)\rMise \xc3\xa0 jour des fichiers: 65% (4014/6175)\rMise \xc3\xa0 jour des fichiers: 66% (4076/6175)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6175)\rMise \xc3\xa0 jour des fichiers: 68% (4199/6175)\rMise \xc3\xa0 jour des fichiers: 69% (4261/6175)\rMise \xc3\xa0 jour des fichiers: 70% (4323/6175)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6175)\rMise \xc3\xa0 jour des fichiers: 72% (4446/6175)\rMise \xc3\xa0 jour des fichiers: 73% (4508/6175)\rMise \xc3\xa0 jour des fichiers: 74% (4570/6175)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6175)\rMise \xc3\xa0 jour des fichiers: 76% (4693/6175)\rMise \xc3\xa0 jour des fichiers: 77% (4755/6175)\rMise \xc3\xa0 jour des fichiers: 78% (4817/6175)\rMise \xc3\xa0 jour des fichiers: 79% (4879/6175)\rMise \xc3\xa0 jour des fichiers: 80% (4940/6175)\rMise \xc3\xa0 jour des fichiers: 81% (5002/6175)\rMise \xc3\xa0 jour des fichiers: 82% (5064/6175)\rMise \xc3\xa0 jour des fichiers: 83% (5126/6175)\rMise \xc3\xa0 jour des fichiers: 84% (5187/6175)\rMise \xc3\xa0 jour des fichiers: 85% (5249/6175)\rMise \xc3\xa0 jour des fichiers: 86% (5311/6175)\rMise \xc3\xa0 jour des fichiers: 87% (5373/6175)\rMise \xc3\xa0 jour des fichiers: 88% (5434/6175)\rMise \xc3\xa0 jour des fichiers: 89% (5496/6175)\rMise \xc3\xa0 jour des fichiers: 90% (5558/6175)\rMise \xc3\xa0 jour des fichiers: 91% (5620/6175)\rMise \xc3\xa0 jour des fichiers: 92% (5681/6175)\rMise \xc3\xa0 jour des fichiers: 93% (5743/6175)\rMise \xc3\xa0 jour des fichiers: 94% (5805/6175)\rMise \xc3\xa0 jour des fichiers: 95% (5867/6175)\rMise \xc3\xa0 jour des fichiers: 96% (5928/6175)\rMise \xc3\xa0 jour des fichiers: 97% (5990/6175)\rMise \xc3\xa0 jour des fichiers: 98% (6052/6175)\rMise \xc3\xa0 jour des fichiers: 99% (6114/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175)\rMise \xc3\xa0 jour des fichiers: 100% (6175/6175), fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-'..b'runners DEBUG 2023-05-03 18:26:52,562 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] (61) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmp1lnw8o38/job_working_directory/000/61/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp1lnw8o38/job_working_directory/000/61/galaxy_61.ec; \n-if [ -f "/tmp/tmp1lnw8o38/job_working_directory/000/61/working/abundance.biom" ] ; then cp "/tmp/tmp1lnw8o38/job_working_directory/000/61/working/abundance.biom" "/tmp/tmp1lnw8o38/job_working_directory/000/61/outputs/galaxy_dataset_b71cc5e6-174b-4877-ab2f-50c9e54ced3d.dat" ; fi; \n-if [ -f "/tmp/tmp1lnw8o38/job_working_directory/000/61/working/seed.fasta" ] ; then cp "/tmp/tmp1lnw8o38/job_working_directory/000/61/working/seed.fasta" "/tmp/tmp1lnw8o38/job_working_directory/000/61/outputs/galaxy_dataset_c6200c47-8aae-4f25-9108-d5de09303397.dat" ; fi; cd \'/tmp/tmp1lnw8o38/job_working_directory/000/61\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-03 18:26:52,583 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] (61) executing job script: /tmp/tmp1lnw8o38/job_working_directory/000/61/galaxy_61.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-03 18:26:56,881 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 132858\n-galaxy.jobs.runners.local DEBUG 2023-05-03 18:26:56,881 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmp1lnw8o38/job_working_directory/000/61/galaxy_61.sh\n-galaxy.jobs DEBUG 2023-05-03 18:26:56,960 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp1lnw8o38/job_working_directory/000/61/outputs/galaxy_dataset_b71cc5e6-174b-4877-ab2f-50c9e54ced3d.dat to /tmp/tmp1lnw8o38/files/b/7/1/dataset_b71cc5e6-174b-4877-ab2f-50c9e54ced3d.dat\n-galaxy.jobs DEBUG 2023-05-03 18:26:56,960 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp1lnw8o38/job_working_directory/000/61/outputs/galaxy_dataset_c6200c47-8aae-4f25-9108-d5de09303397.dat to /tmp/tmp1lnw8o38/files/c/6/2/dataset_c6200c47-8aae-4f25-9108-d5de09303397.dat\n-galaxy.model.metadata DEBUG 2023-05-03 18:26:57,048 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 84\n-galaxy.model.metadata DEBUG 2023-05-03 18:26:57,069 [pN:main.1,p:6319,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 85\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 10 test(s) - out of 22 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_affiliation_filters (Test #1): passed\n-FROGS_affiliation_filters (Test #2): passed\n-FROGS_affiliation_postprocess (Test #1): passed\n-FROGS_affiliation_stats (Test #1): passed\n-FROGS_biom_to_stdBiom (Test #1): passed\n-FROGS_biom_to_tsv (Test #1): passed\n-FROGS_cluster_filters (Test #1): failed\n-FROGS_clustering (Test #1): failed\n-FROGS_demultiplex (Test #1): passed\n-FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n-FROGSSTAT_Phyloseq_Beta_Diversity (Test #1): failed\n-FROGSSTAT_Phyloseq_Sample_Clustering (Test #1): failed\n-FROGSSTAT_Phyloseq_Composition_Visualisation (Test #1): passed\n-FROGSSTAT_Phyloseq_Import_Data (Test #1): passed\n-FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance (Test #1): failed\n-FROGSSTAT_Phyloseq_Structure_Visualisation (Test #1): passed\n-FROGS_preprocess (Test #1): failed\n-FROGS_preprocess (Test #2): failed\n-FROGS_remove_chimera (Test #1): passed\n-FROGS_taxonomic_affiliation (Test #1): failed\n-FROGS_Tree (Test #1): failed\n-FROGS_tsv_to_biom (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/affiliation_filters.xml -Applying linter tests... CHECK -.. CHECK: 2 test(s) found. -Applying linter output... CHECK -.. INFO: 5 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 13 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS Affiliation Filters]. -.. CHECK: Tool defines an id [FROGS_affiliation_filters]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.test.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_filters.test.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,2139 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp9qcmzckb/galaxy-dev\n-Clonage dans \'/tmp/tmp9qcmzckb/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'y/000/6/outputs/galaxy_dataset_c1e7acbe-eaaa-4955-b77c-2c777fe2f343.dat" ; fi; \n-if [ -f "/tmp/tmp9qcmzckb/job_working_directory/000/6/working/report.html" ] ; then cp "/tmp/tmp9qcmzckb/job_working_directory/000/6/working/report.html" "/tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_2019c937-3bcb-4b7a-a326-b14c4ce97e2d.dat" ; fi; cd \'/tmp/tmp9qcmzckb/job_working_directory/000/6\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-25 10:07:35,439 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] (6) executing job script: /tmp/tmp9qcmzckb/job_working_directory/000/6/galaxy_6.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-25 10:07:39,758 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 126528\n-galaxy.jobs.runners.local DEBUG 2023-04-25 10:07:39,758 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmp9qcmzckb/job_working_directory/000/6/galaxy_6.sh\n-galaxy.jobs DEBUG 2023-04-25 10:07:39,815 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_595edf96-87d7-45f4-ae55-5e2a8f60c7d8.dat to /tmp/tmp9qcmzckb/files/5/9/5/dataset_595edf96-87d7-45f4-ae55-5e2a8f60c7d8.dat\n-galaxy.jobs DEBUG 2023-04-25 10:07:39,815 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_02e54cad-416c-40a5-b04f-1c9a2e7fe716.dat to /tmp/tmp9qcmzckb/files/0/2/e/dataset_02e54cad-416c-40a5-b04f-1c9a2e7fe716.dat\n-galaxy.jobs DEBUG 2023-04-25 10:07:39,817 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_6035da0d-daec-46e8-a9ac-65b28363051f.dat to /tmp/tmp9qcmzckb/files/6/0/3/dataset_6035da0d-daec-46e8-a9ac-65b28363051f.dat\n-galaxy.jobs DEBUG 2023-04-25 10:07:39,817 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_c1e7acbe-eaaa-4955-b77c-2c777fe2f343.dat to /tmp/tmp9qcmzckb/files/c/1/e/dataset_c1e7acbe-eaaa-4955-b77c-2c777fe2f343.dat\n-galaxy.jobs DEBUG 2023-04-25 10:07:39,820 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp9qcmzckb/job_working_directory/000/6/outputs/galaxy_dataset_2019c937-3bcb-4b7a-a326-b14c4ce97e2d.dat to /tmp/tmp9qcmzckb/files/2/0/1/dataset_2019c937-3bcb-4b7a-a326-b14c4ce97e2d.dat\n-galaxy.model.metadata DEBUG 2023-04-25 10:07:39,864 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 9\n-galaxy.model.metadata DEBUG 2023-04-25 10:07:39,873 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 10\n-galaxy.model.metadata DEBUG 2023-04-25 10:07:39,882 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 11\n-galaxy.model.metadata DEBUG 2023-04-25 10:07:39,891 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 12\n-galaxy.model.metadata DEBUG 2023-04-25 10:07:39,900 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 13\n-galaxy.jobs DEBUG 2023-04-25 10:07:39,983 [pN:main.1,p:125639,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 6 executed (175.968 ms)\n-\n-galaxy.tool_util.verify INFO: ## files diff on \'/tmp/tmp7b94ceug07-affiliation_deleted.html\' and \'/tmp/tmpya0eqxsh07-affiliation_deleted.html\': lines_diff = 0, found diff = 22\n-Shut down\n-supervisord has terminated\n-There were problems with 2 test(s) - out of 2 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_affiliation_filters (Test #1): failed\n-FROGS_affiliation_filters (Test #2): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/affiliation_postprocess.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 6 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS Affiliation postprocess]. -.. CHECK: Tool defines an id [FROGS_affiliation_postprocess]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.test.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_postprocess.test.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1889 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmppi6b2sqi/galaxy-dev\n-Clonage dans \'/tmp/tmppi6b2sqi/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'or was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; affiliation_postprocess.py --identity 99.0 --coverage 99.0 --input-biom \'/tmp/tmppi6b2sqi/files/6/9/b/dataset_69bad65a-6880-44a6-a703-46cd3ec77d1a.dat\' --input-fasta \'/tmp/tmppi6b2sqi/files/9/6/a/dataset_96ab65c6-95ab-49c2-ba7b-e40554eefe31.dat\' --output-biom \'/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_dc3db348-241c-4e43-bab5-082edcccca7e.dat\' --output-fasta \'/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_f6a5f1c0-aa78-46d7-b45f-d5b2070860d4.dat\' --output-compo \'/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_27919559-054e-4612-9447-e22347219a85.dat\']\n-galaxy.jobs.runners DEBUG 2023-04-25 10:08:39,296 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] (3) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmppi6b2sqi/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmppi6b2sqi/job_working_directory/000/3/galaxy_3.ec; \n-if [ -f "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/affiliation.biom" ] ; then cp "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/affiliation.biom" "/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_dc3db348-241c-4e43-bab5-082edcccca7e.dat" ; fi; \n-if [ -f "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/sequences.fasta" ] ; then cp "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/sequences.fasta" "/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_f6a5f1c0-aa78-46d7-b45f-d5b2070860d4.dat" ; fi; \n-if [ -f "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/aggregation_composition.txt" ] ; then cp "/tmp/tmppi6b2sqi/job_working_directory/000/3/working/aggregation_composition.txt" "/tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_27919559-054e-4612-9447-e22347219a85.dat" ; fi; cd \'/tmp/tmppi6b2sqi/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-25 10:08:39,310 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] (3) executing job script: /tmp/tmppi6b2sqi/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-25 10:08:44,022 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 127528\n-galaxy.jobs.runners.local DEBUG 2023-04-25 10:08:44,022 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmppi6b2sqi/job_working_directory/000/3/galaxy_3.sh\n-galaxy.jobs DEBUG 2023-04-25 10:08:44,080 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_dc3db348-241c-4e43-bab5-082edcccca7e.dat to /tmp/tmppi6b2sqi/files/d/c/3/dataset_dc3db348-241c-4e43-bab5-082edcccca7e.dat\n-galaxy.jobs DEBUG 2023-04-25 10:08:44,080 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_f6a5f1c0-aa78-46d7-b45f-d5b2070860d4.dat to /tmp/tmppi6b2sqi/files/f/6/a/dataset_f6a5f1c0-aa78-46d7-b45f-d5b2070860d4.dat\n-galaxy.jobs DEBUG 2023-04-25 10:08:44,081 [pN:main.1,p:127427,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmppi6b2sqi/job_working_directory/000/3/outputs/galaxy_dataset_27919559-054e-4612-9447-e22347219a85.dat to /tmp/tmppi6b2sqi/files/2/7/9/dataset_27919559-054e-4612-9447-e22347219a85.dat\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_affiliation_postprocess (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/affiliation_stats.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 8 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS_6_Affiliation_Stat]. -.. CHECK: Tool defines an id [FROGS_affiliation_stats]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.test.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/affiliation_stats.test.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,992 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp6sl3s_05/galaxy-dev\n-Clonage dans \'/tmp/tmp6sl3s_05/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vdar'..b'patching to planemo_runner runner\n-galaxy.jobs DEBUG 2023-04-25 10:09:43,253 [pN:main.1,p:128442,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: planemo_dest)\n-galaxy.jobs DEBUG 2023-04-25 10:09:43,259 [pN:main.1,p:128442,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /tmp/tmp6sl3s_05/job_working_directory/000/2\n-galaxy.jobs.runners DEBUG 2023-04-25 10:09:43,276 [pN:main.1,p:128442,tN:JobHandlerQueue.monitor_thread] Job [2] queued (72.382 ms)\n-galaxy.jobs.handler INFO 2023-04-25 10:09:43,286 [pN:main.1,p:128442,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n-galaxy.jobs DEBUG 2023-04-25 10:09:43,374 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] Job wrapper for Job [2] prepared (82.886 ms)\n-galaxy.tool_util.deps DEBUG 2023-04-25 10:09:43,375 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] Using dependency frogs version 4.1.0 of type conda\n-galaxy.tool_util.deps DEBUG 2023-04-25 10:09:43,375 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] Using dependency frogs version 4.1.0 of type conda\n-galaxy.jobs.command_factory INFO 2023-04-25 10:09:43,392 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] Built script [/tmp/tmp6sl3s_05/job_working_directory/000/2/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; affiliation_stats.py --input-biom \'/tmp/tmp6sl3s_05/files/0/8/c/dataset_08cb8a17-6762-4e50-b5de-4602c2fef700.dat\' --output-file \'/tmp/tmp6sl3s_05/job_working_directory/000/2/outputs/galaxy_dataset_1a79590c-5959-4e26-a94c-eb1d3d789546.dat\' --taxonomic-ranks Domain Phylum Class Order Family Genus Species --rarefaction-ranks Family Genus Species --multiple-tag \'blast_affiliations\' --tax-consensus-tag \'blast_taxonomy\' --identity-tag \'perc_identity\' --coverage-tag \'perc_query_coverage\']\n-galaxy.jobs.runners DEBUG 2023-04-25 10:09:43,464 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmp6sl3s_05/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp6sl3s_05/job_working_directory/000/2/galaxy_2.ec; \n-if [ -f "/tmp/tmp6sl3s_05/job_working_directory/000/2/working/summary.html" ] ; then cp "/tmp/tmp6sl3s_05/job_working_directory/000/2/working/summary.html" "/tmp/tmp6sl3s_05/job_working_directory/000/2/outputs/galaxy_dataset_1a79590c-5959-4e26-a94c-eb1d3d789546.dat" ; fi; cd \'/tmp/tmp6sl3s_05/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-25 10:09:43,479 [pN:main.1,p:128442,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmp6sl3s_05/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.tool_util.verify INFO: ## files diff on \'/tmp/tmp_oyu80z611-affiliationsStat.html\' and \'/tmp/tmp1flu7_ok11-affiliationsStat.html\': lines_diff = 2, found diff = 24\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_affiliation_stats (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/biom_to_stdBiom.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 1 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS BIOM to std BIOM]. -.. CHECK: Tool defines an id [FROGS_biom_to_stdBiom]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.test.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/biom_to_stdBiom.test.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1003 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp2vc8jplr/galaxy-dev\n-Clonage dans \'/tmp/tmp2vc8jplr/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b' else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; biom_to_stdBiom.py --input-biom \'/tmp/tmp2vc8jplr/files/b/e/1/dataset_be142786-3b8d-42d8-a52e-e159f016b5aa.dat\' --output-biom \'/tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_9b56e9ef-f202-48bb-a0e4-572245eae18f.dat\' --output-metadata \'/tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_2a18acad-24f5-46f0-9fd8-9bcd0550af07.dat\']\n-galaxy.jobs.runners DEBUG 2023-04-25 10:10:41,741 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmp2vc8jplr/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp2vc8jplr/job_working_directory/000/2/galaxy_2.ec; \n-if [ -f "/tmp/tmp2vc8jplr/job_working_directory/000/2/working/abundance.biom" ] ; then cp "/tmp/tmp2vc8jplr/job_working_directory/000/2/working/abundance.biom" "/tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_9b56e9ef-f202-48bb-a0e4-572245eae18f.dat" ; fi; \n-if [ -f "/tmp/tmp2vc8jplr/job_working_directory/000/2/working/blast_details.tsv" ] ; then cp "/tmp/tmp2vc8jplr/job_working_directory/000/2/working/blast_details.tsv" "/tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_2a18acad-24f5-46f0-9fd8-9bcd0550af07.dat" ; fi; cd \'/tmp/tmp2vc8jplr/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-25 10:10:41,757 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmp2vc8jplr/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-25 10:10:45,694 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 129418\n-galaxy.jobs.runners.local DEBUG 2023-04-25 10:10:45,695 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmp2vc8jplr/job_working_directory/000/2/galaxy_2.sh\n-galaxy.jobs DEBUG 2023-04-25 10:10:45,742 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_9b56e9ef-f202-48bb-a0e4-572245eae18f.dat to /tmp/tmp2vc8jplr/files/9/b/5/dataset_9b56e9ef-f202-48bb-a0e4-572245eae18f.dat\n-galaxy.jobs DEBUG 2023-04-25 10:10:45,742 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp2vc8jplr/job_working_directory/000/2/outputs/galaxy_dataset_2a18acad-24f5-46f0-9fd8-9bcd0550af07.dat to /tmp/tmp2vc8jplr/files/2/a/1/dataset_2a18acad-24f5-46f0-9fd8-9bcd0550af07.dat\n-galaxy.model.metadata DEBUG 2023-04-25 10:10:45,779 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 2\n-galaxy.model.metadata DEBUG 2023-04-25 10:10:45,787 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.jobs DEBUG 2023-04-25 10:10:45,862 [pN:main.1,p:129364,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 2 executed (125.434 ms)\n-\n-galaxy.tool_util.verify INFO: ## files diff on \'/tmp/tmp7mjnslv513-affiliation_multihit.tsv\' and \'/tmp/tmp9q6ya5ku13-affiliation_multihit.tsv\': lines_diff = 0, found diff = 97\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_biom_to_stdBiom (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/biom_to_tsv.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS BIOM to TSV]. -.. CHECK: Tool defines an id [FROGS_biom_to_tsv]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.test.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/biom_to_tsv.test.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1825 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpe5j6sxz0/galaxy-dev\n-Clonage dans \'/tmp/tmpe5j6sxz0/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'ers.local DEBUG 2023-04-25 10:11:33,704 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] (1) executing job script: /tmp/tmpe5j6sxz0/job_working_directory/000/1/galaxy_1.sh\n-galaxy.jobs.mapper DEBUG 2023-04-25 10:11:34,350 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: upload_dest\n-galaxy.jobs.handler DEBUG 2023-04-25 10:11:34,357 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to planemo_runner runner\n-galaxy.jobs DEBUG 2023-04-25 10:11:34,488 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: upload_dest)\n-galaxy.jobs DEBUG 2023-04-25 10:11:34,497 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /tmp/tmpe5j6sxz0/job_working_directory/000/2\n-galaxy.jobs.runners DEBUG 2023-04-25 10:11:34,513 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] Job [2] queued (155.352 ms)\n-galaxy.jobs.handler INFO 2023-04-25 10:11:34,523 [pN:main.1,p:130255,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n-galaxy.jobs DEBUG 2023-04-25 10:11:34,647 [pN:main.1,p:130255,tN:LocalRunner.work_thread-1] Job wrapper for Job [2] prepared (109.936 ms)\n-galaxy.jobs.command_factory INFO 2023-04-25 10:11:34,663 [pN:main.1,p:130255,tN:LocalRunner.work_thread-1] Built script [/tmp/tmpe5j6sxz0/job_working_directory/000/2/tool_script.sh] for tool command [python \'/tmp/tmpe5j6sxz0/galaxy-dev/tools/data_source/upload.py\' \'/tmp/tmpe5j6sxz0/galaxy-dev\' \'/tmp/tmpe5j6sxz0/job_working_directory/000/2/registry.xml\' \'/tmp/tmpe5j6sxz0/tmp/upload_params_4dov0ik0\' \'2:/tmp/tmpe5j6sxz0/job_working_directory/000/2/working/dataset_30175cbd-5fac-4cdb-b7e6-37e4713ed524_files:/tmp/tmpe5j6sxz0/job_working_directory/000/2/outputs/galaxy_dataset_30175cbd-5fac-4cdb-b7e6-37e4713ed524.dat\']\n-\n-galaxy.jobs.runners DEBUG 2023-04-25 10:11:34,709 [pN:main.1,p:130255,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpe5j6sxz0/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpe5j6sxz0/job_working_directory/000/2/galaxy_2.ec; cd \'/tmp/tmpe5j6sxz0/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-25 10:11:34,726 [pN:main.1,p:130255,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmpe5j6sxz0/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-25 10:11:37,539 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 130274\n-galaxy.jobs.runners.local DEBUG 2023-04-25 10:11:37,539 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpe5j6sxz0/job_working_directory/000/1/galaxy_1.sh\n-galaxy.jobs DEBUG 2023-04-25 10:11:37,638 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpe5j6sxz0/job_working_directory/000/1/outputs/galaxy_dataset_8be40f4f-af9e-4fc5-a44a-5745106653c7.dat to /tmp/tmpe5j6sxz0/files/8/b/e/dataset_8be40f4f-af9e-4fc5-a44a-5745106653c7.dat\n-\n-galaxy.model.metadata DEBUG 2023-04-25 10:11:37,703 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 1\n-galaxy.jobs DEBUG 2023-04-25 10:11:37,785 [pN:main.1,p:130255,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 1 executed (187.283 ms)\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_biom_to_tsv (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/cluster_filters.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 4 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 13 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS_4 Cluster filters]. -.. CHECK: Tool defines an id [FROGS_cluster_filters]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.test.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/cluster_filters.test.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1049 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpwby5bixe/galaxy-dev\n-Clonage dans \'/tmp/tmpwby5bixe/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b"23-04-25 10:12:47,421 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --strict-channel-priority --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-2e551f2af3517c80384199d3fff6b06c5fa3d12c3c5277abd509d92437d55a28 frogs=4.1.0 blast=2.10\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:13:09,029 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-2e551f2af3517c80384199d3fff6b06c5fa3d12c3c5277abd509d92437d55a28 frogs=4.1.0 blast=2.10\n-\n-galaxy.tool_util.deps.resolvers.conda DEBUG 2023-04-25 10:13:13,057 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Removing failed conda install of [CondaTarget[frogs,version=4.1.0], CondaTarget[blast,version=2.10]]\n-galaxy.tool_util.deps DEBUG 2023-04-25 10:13:13,057 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Using dependency frogs version 4.1.0 of type conda\n-galaxy.tool_util.deps DEBUG 2023-04-25 10:13:13,057 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Using dependency blast version 2.10 of type conda\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:13:13,058 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --strict-channel-priority --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-2e551f2af3517c80384199d3fff6b06c5fa3d12c3c5277abd509d92437d55a28 frogs=4.1.0 blast=2.10\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:13:22,977 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-2e551f2af3517c80384199d3fff6b06c5fa3d12c3c5277abd509d92437d55a28 frogs=4.1.0 blast=2.10\n-\n-galaxy.tool_util.deps.resolvers.conda DEBUG 2023-04-25 10:13:31,937 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Removing failed conda install of [CondaTarget[frogs,version=4.1.0], CondaTarget[blast,version=2.10]]\n-galaxy.tool_util.deps DEBUG 2023-04-25 10:13:31,937 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Using dependency frogs version 4.1.0 of type conda\n-galaxy.tool_util.deps DEBUG 2023-04-25 10:13:31,937 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Using dependency blast version 2.10 of type conda\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:13:31,937 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda list --name __frogs@4.1.0 --export > '/tmp/tmpwby5bixe/tmp/jobdeps72lihs9lae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0'\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:13:36,783 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --strict-channel-priority --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmpwby5bixe/deps/_cache/7aceb47c --file /tmp/tmpwby5bixe/tmp/jobdeps72lihs9lae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0\n-\n-galaxy.tool_util.deps.conda_util DEBUG 2023-04-25 10:18:09,666 [pN:main.1,p:130465,tN:LocalRunner.work_thread-2] Executing command: /home/vdarbot/miniconda3/bin/conda create -y --quiet --override-channels --channel vincentdarbot --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /tmp/tmpwby5bixe/deps/_cache/7aceb47c --file /tmp/tmpwby5bixe/tmp/jobdeps72lihs9lae10fabd7900a582561bb202e423239917e98ee05d6551b525bd730a540b16c1/__frogs@4.1.0\n-\n-\n-Aborted!\n-Shut down\n-\n-Aborted!\n" |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/cluster_stats.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/cluster_stats.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/cluster_stats.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 1 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS_Cluster_Stat]. -.. CHECK: Tool defines an id [FROGS_cluster_stats]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/clustering.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/clustering.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/clustering.xml -Applying linter tests... CHECK -.. CHECK: 2 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 7 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS_2 Clustering swarm]. -.. CHECK: Tool defines an id [FROGS_clustering]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/clustering.test.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/clustering.test.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,12 +0,0 @@ -Traceback (most recent call last): - File "/home/vdarbot/miniconda3/bin/planemo", line 5, in <module> - from planemo.cli import planemo - File "/home/vdarbot/miniconda3/lib/python3.9/site-packages/planemo/cli.py", line 24, in <module> - from planemo.galaxy import profiles - File "/home/vdarbot/miniconda3/lib/python3.9/site-packages/planemo/galaxy/__init__.py", line 4, in <module> - File "/home/vdarbot/miniconda3/lib/python3.9/site-packages/planemo/galaxy/config.py", line 29, in <module> - File "/home/vdarbot/miniconda3/lib/python3.9/site-packages/galaxy/tool_util/deps/__init__.py", line 17, in <module> - File "/home/vdarbot/miniconda3/lib/python3.9/site-packages/galaxy/util/__init__.py", line 63, in <module> - File "src/lxml/etree.pyx", line 96, in init lxml.etree - File "/home/vdarbot/miniconda3/lib/python3.9/abc.py", line 107, in __new__ -KeyboardInterrupt |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/demultiplex.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/demultiplex.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/demultiplex.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 7 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS_0 Demultiplex reads]. -.. CHECK: Tool defines an id [FROGS_demultiplex]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/deseq2_preprocess.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/deseq2_preprocess.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,23 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/deseq2_preprocess.xml -Failed linting -Applying linter tests... FAIL -.. ERROR: Test 1: Found output tag with unknown name [dds], valid names ['dds_asv', 'dds_function', 'phyloseq'] -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 8 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSSTAT DESeq2 Preprocess]. -.. CHECK: Tool defines an id [FROGSSTAT_DESeq2_Preprocess]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... FAIL -.. ERROR: Invalid XML found in file: deseq2_preprocess.xml. Errors [/tmp/tmpjg7yzk7o:30:0:ERROR:SCHEMASV:SCHEMAV_CVC_COMPLEX_TYPE_2_3: Element 'inputs': Character content other than whitespace is not allowed because the content type is 'element-only'.] |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/deseq2_visualisation.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/deseq2_visualisation.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/deseq2_visualisation.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 8 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSSTAT DESeq2 Visualisation]. -.. CHECK: Tool defines an id [FROGSSTAT_DESeq2_Visualisation]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_functions.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_functions.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,28 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/frogsfunc_functions.xml -Failed linting -Applying linter tests... FAIL -.. ERROR: Test 1: Test param function not found in the inputs -.. ERROR: Test 1: Test param marker not found in the inputs -.. ERROR: Test 1: Test param min_reads not found in the inputs -.. ERROR: Test 1: Test param min_samples not found in the inputs -.. ERROR: Test 1: Test param strat not found in the inputs -.. ERROR: Test 1: Found output tag with unknown name [output_function_abund], valid names ['summary_file', 'output_biom', 'output_fasta', 'output_otu_norm', 'output_weighted', 'output_excluded', 'output_copy_ec_abund', 'output_copy_ko_abund', 'output_copy_cog_abund', 'output_copy_pfam_abund', 'output_copy_tigrfam_abund', 'output_copy_pheno_abund', 'output_function_ec_abund', 'output_function_ko_abund', 'output_function_cog_abund', 'output_function_pfam_abund', 'output_function_tigrfam_abund', 'output_function_pheno_abund'] -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 18 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 10 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSFUNC_2_functions]. -.. CHECK: Tool defines an id [FROGSFUNC_step3_functions]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_pathways.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_pathways.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/frogsfunc_pathways.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 4 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSFUNC_3_pathways]. -.. CHECK: Tool defines an id [FROGSFUNC_step4_pathways]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_placeseqs.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/frogsfunc_placeseqs.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/frogsfunc_placeseqs.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 7 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 5 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSFUNC_1_placeseqs_and_copynumbers]. -.. CHECK: Tool defines an id [FROGSFUNC_step1_placeseqs]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/itsx.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/itsx.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,23 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/itsx.xml -Failed linting -Applying linter tests... FAIL -.. ERROR: Test 1: Test param trim_sequence not found in the inputs -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 4 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 5 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS ITSx]. -.. CHECK: Tool defines an id [FROGS_itsx]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/normalisation.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/normalisation.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/normalisation.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 5 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS Abundance normalisation]. -.. CHECK: Tool defines an id [FROGS_normalisation]. -.. CHECK: Tool targets 16.01 Galaxy profile. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_alpha_diversity.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_alpha_diversity.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_alpha_diversity.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Alpha Diversity]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Alpha_Diversity]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_beta_diversity.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_beta_diversity.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_beta_diversity.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 4 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Beta Diversity]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Beta_Diversity]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_clustering.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_clustering.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_clustering.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Sample Clustering]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Sample_Clustering]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_composition.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_composition.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_composition.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 6 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Composition Visualisation]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Composition_Visualisation]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_import_data.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_import_data.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_import_data.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 5 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Import Data]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Import_Data]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_manova.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_manova.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_manova.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Multivariate Analysis Of Variance]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_structure.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/phyloseq_structure.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/phyloseq_structure.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 1 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 4 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGSSTAT Phyloseq Structure Visualisation]. -.. CHECK: Tool defines an id [FROGSSTAT_Phyloseq_Structure_Visualisation]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/preprocess.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/preprocess.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/preprocess.xml -Applying linter tests... CHECK -.. CHECK: 2 test(s) found. -Applying linter output... CHECK -.. INFO: 3 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 44 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS_1 Pre-process]. -.. CHECK: Tool defines an id [FROGS_preprocess]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/remove_chimera.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/remove_chimera.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/remove_chimera.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 4 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 4 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS_3 Remove chimera]. -.. CHECK: Tool defines an id [FROGS_remove_chimera]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/taxonomic_affiliation.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/taxonomic_affiliation.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/taxonomic_affiliation.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 5 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS_5 Taxonomic affiliation]. -.. CHECK: Tool defines an id [FROGS_taxonomic_affiliation]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/tree.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/tree.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/tree.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 2 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS Tree]. -.. CHECK: Tool defines an id [FROGS_Tree]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.1.0_vincentdarbot/tsv_to_biom.lint.log --- a/test-data/planemo_test_4.1.0_vincentdarbot/tsv_to_biom.lint.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
@@ -1,21 +0,0 @@ -Linting tool /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/tsv_to_biom.xml -Applying linter tests... CHECK -.. CHECK: 1 test(s) found. -Applying linter output... CHECK -.. INFO: 2 outputs found. -Applying linter inputs... CHECK -.. INFO: Found 3 input parameters. -Applying linter help... CHECK -.. CHECK: Tool contains help section. -.. CHECK: Help contains valid reStructuredText. -Applying linter general... CHECK -.. CHECK: Tool defines a version [4.1.0+galaxy1]. -.. CHECK: Tool defines a name [FROGS TSV_to_BIOM]. -.. CHECK: Tool defines an id [FROGS_tsv_to_biom]. -.. CHECK: Tool specifies profile version [20.05]. -Applying linter command... CHECK -.. INFO: Tool contains a command. -Applying linter citations... CHECK -.. CHECK: Found 2 likely valid citations. -Applying linter tool_xsd... CHECK -.. INFO: File validates against XML schema. |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_4.log --- a/test-data/planemo_test_4.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,6086 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpvrixslsg/galaxy-dev\n-Clonage dans \'/tmp/tmpvrixslsg/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'er.work_thread-0] (83) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpvrixslsg/job_working_directory/000/83/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpvrixslsg/job_working_directory/000/83/galaxy_83.ec; \n-if [ -f "/tmp/tmpvrixslsg/job_working_directory/000/83/working/abundance.biom" ] ; then cp "/tmp/tmpvrixslsg/job_working_directory/000/83/working/abundance.biom" "/tmp/tmpvrixslsg/job_working_directory/000/83/outputs/galaxy_dataset_5a468301-746c-42ad-bcf0-7ddd00ea53e5.dat" ; fi; \n-if [ -f "/tmp/tmpvrixslsg/job_working_directory/000/83/working/seed.fasta" ] ; then cp "/tmp/tmpvrixslsg/job_working_directory/000/83/working/seed.fasta" "/tmp/tmpvrixslsg/job_working_directory/000/83/outputs/galaxy_dataset_5049f307-1911-43a7-a62f-fcba4c73ff64.dat" ; fi; cd \'/tmp/tmpvrixslsg/job_working_directory/000/83\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-04 14:20:47,839 [pN:main.1,p:183534,tN:LocalRunner.work_thread-0] (83) executing job script: /tmp/tmpvrixslsg/job_working_directory/000/83/galaxy_83.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-04 14:20:50,912 [pN:main.1,p:183534,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 267154\n-galaxy.jobs.runners.local DEBUG 2023-05-04 14:20:50,913 [pN:main.1,p:183534,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpvrixslsg/job_working_directory/000/83/galaxy_83.sh\n-galaxy.jobs DEBUG 2023-05-04 14:20:50,948 [pN:main.1,p:183534,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpvrixslsg/job_working_directory/000/83/outputs/galaxy_dataset_5a468301-746c-42ad-bcf0-7ddd00ea53e5.dat to /tmp/tmpvrixslsg/files/5/a/4/dataset_5a468301-746c-42ad-bcf0-7ddd00ea53e5.dat\n-galaxy.jobs DEBUG 2023-05-04 14:20:50,948 [pN:main.1,p:183534,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpvrixslsg/job_working_directory/000/83/outputs/galaxy_dataset_5049f307-1911-43a7-a62f-fcba4c73ff64.dat to /tmp/tmpvrixslsg/files/5/0/4/dataset_5049f307-1911-43a7-a62f-fcba4c73ff64.dat\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 10 test(s) - out of 31 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_affiliation_filters (Test #1): passed\n-FROGS_affiliation_filters (Test #2): passed\n-FROGS_affiliation_postprocess (Test #1): passed\n-FROGS_affiliation_stats (Test #1): passed\n-FROGS_biom_to_stdBiom (Test #1): passed\n-FROGS_biom_to_tsv (Test #1): passed\n-FROGS_cluster_filters (Test #1): failed\n-FROGS_clustering (Test #1): passed\n-FROGS_clustering (Test #2): passed\n-FROGS_cluster_stats (Test #1): passed\n-FROGS_demultiplex (Test #1): passed\n-FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n-FROGSSTAT_DESeq2_Visualisation (Test #1): failed\n-FROGSFUNC_step3_functions (Test #1): failed\n-FROGSFUNC_step4_pathways (Test #1): failed\n-FROGSFUNC_step1_placeseqs (Test #1): failed\n-FROGS_itsx (Test #1): passed\n-FROGS_normalisation (Test #1): passed\n-FROGSSTAT_Phyloseq_Alpha_Diversity (Test #1): passed\n-FROGSSTAT_Phyloseq_Beta_Diversity (Test #1): failed\n-FROGSSTAT_Phyloseq_Sample_Clustering (Test #1): passed\n-FROGSSTAT_Phyloseq_Composition_Visualisation (Test #1): passed\n-FROGSSTAT_Phyloseq_Import_Data (Test #1): passed\n-FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance (Test #1): passed\n-FROGSSTAT_Phyloseq_Structure_Visualisation (Test #1): passed\n-FROGS_preprocess (Test #1): failed\n-FROGS_preprocess (Test #2): failed\n-FROGS_remove_chimera (Test #1): passed\n-FROGS_taxonomic_affiliation (Test #1): failed\n-FROGS_Tree (Test #1): passed\n-FROGS_tsv_to_biom (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_5.log --- a/test-data/planemo_test_5.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,17841 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpu_fgppyy/galaxy-dev\n-Clonage dans \'/tmp/tmpu_fgppyy/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vd'..b", job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id \n-FROM history_dataset_collection_association, job_to_output_dataset_collection \n-WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.metadata, history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata_deferred, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id \n-FROM history_dataset_association, job_to_output_dataset \n-WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 \n-FROM job \n-WHERE job.state IN (?, ?, ?) AND job.handler = ?]\n-[parameters: (<states.DELETED_NEW: 'deleted_new'>, <states.DELETING: 'deleting'>, <states.STOPPING: 'stop'>, 'main.1')]\n-(Background on this error at: https://sqlalche.me/e/14/e3q8)\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 3 test(s) - out of 16 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_affiliation_filters (Test #1): passed\n-FROGS_affiliation_filters (Test #2): passed\n-FROGS_affiliation_postprocess (Test #1): passed\n-FROGS_affiliation_stats (Test #1): passed\n-FROGS_biom_to_stdBiom (Test #1): passed\n-FROGS_biom_to_tsv (Test #1): passed\n-FROGS_cluster_filters (Test #1): passed\n-FROGS_clustering (Test #1): passed\n-FROGS_clustering (Test #2): passed\n-FROGS_cluster_stats (Test #1): passed\n-FROGS_demultiplex (Test #1): passed\n-FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n-FROGSSTAT_DESeq2_Visualisation (Test #1): passed\n-FROGSFUNC_step3_functions (Test #1): passed\n-FROGSFUNC_step4_pathways (Test #1): failed\n-FROGSFUNC_step1_placeseqs (Test #1): failed\n" |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/planemo_test_6.log --- a/test-data/planemo_test_6.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,6602 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmppgarrkg4/galaxy-dev\n-Clonage dans \'/tmp/tmppgarrkg4/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'tmp/tmppgarrkg4/job_working_directory/000/88/galaxy_88.ec; \n-if [ -f "/tmp/tmppgarrkg4/job_working_directory/000/88/working/abundance.biom" ] ; then cp "/tmp/tmppgarrkg4/job_working_directory/000/88/working/abundance.biom" "/tmp/tmppgarrkg4/job_working_directory/000/88/outputs/galaxy_dataset_4e1c8324-7bde-462f-9fc0-01789f3287a0.dat" ; fi; \n-if [ -f "/tmp/tmppgarrkg4/job_working_directory/000/88/working/seed.fasta" ] ; then cp "/tmp/tmppgarrkg4/job_working_directory/000/88/working/seed.fasta" "/tmp/tmppgarrkg4/job_working_directory/000/88/outputs/galaxy_dataset_bc63d7f9-f46a-4cb9-85c8-261c177d796f.dat" ; fi; cd \'/tmp/tmppgarrkg4/job_working_directory/000/88\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-09 13:02:49,951 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] (88) executing job script: /tmp/tmppgarrkg4/job_working_directory/000/88/galaxy_88.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 13:02:54,169 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 159506\n-galaxy.jobs.runners.local DEBUG 2023-05-09 13:02:54,169 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmppgarrkg4/job_working_directory/000/88/galaxy_88.sh\n-galaxy.jobs DEBUG 2023-05-09 13:02:54,213 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmppgarrkg4/job_working_directory/000/88/outputs/galaxy_dataset_4e1c8324-7bde-462f-9fc0-01789f3287a0.dat to /tmp/tmppgarrkg4/files/4/e/1/dataset_4e1c8324-7bde-462f-9fc0-01789f3287a0.dat\n-galaxy.jobs DEBUG 2023-05-09 13:02:54,213 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmppgarrkg4/job_working_directory/000/88/outputs/galaxy_dataset_bc63d7f9-f46a-4cb9-85c8-261c177d796f.dat to /tmp/tmppgarrkg4/files/b/c/6/dataset_bc63d7f9-f46a-4cb9-85c8-261c177d796f.dat\n-galaxy.model.metadata DEBUG 2023-05-09 13:02:54,265 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 133\n-galaxy.model.metadata DEBUG 2023-05-09 13:02:54,279 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 134\n-\n-galaxy.jobs DEBUG 2023-05-09 13:02:54,498 [pN:main.1,p:60141,tN:LocalRunner.work_thread-2] job_wrapper.finish for job 88 executed (295.746 ms)\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 4 test(s) - out of 31 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_affiliation_filters (Test #1): passed\n-FROGS_affiliation_filters (Test #2): passed\n-FROGS_affiliation_postprocess (Test #1): passed\n-FROGS_affiliation_stats (Test #1): passed\n-FROGS_biom_to_stdBiom (Test #1): passed\n-FROGS_biom_to_tsv (Test #1): passed\n-FROGS_cluster_filters (Test #1): passed\n-FROGS_clustering (Test #1): passed\n-FROGS_clustering (Test #2): passed\n-FROGS_cluster_stats (Test #1): passed\n-FROGS_demultiplex (Test #1): passed\n-FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n-FROGSSTAT_DESeq2_Visualisation (Test #1): passed\n-FROGSFUNC_step3_functions (Test #1): passed\n-FROGSFUNC_step4_pathways (Test #1): passed\n-FROGSFUNC_step1_placeseqs (Test #1): failed\n-FROGS_itsx (Test #1): passed\n-FROGS_normalisation (Test #1): passed\n-FROGSSTAT_Phyloseq_Alpha_Diversity (Test #1): passed\n-FROGSSTAT_Phyloseq_Beta_Diversity (Test #1): passed\n-FROGSSTAT_Phyloseq_Sample_Clustering (Test #1): passed\n-FROGSSTAT_Phyloseq_Composition_Visualisation (Test #1): passed\n-FROGSSTAT_Phyloseq_Import_Data (Test #1): passed\n-FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance (Test #1): passed\n-FROGSSTAT_Phyloseq_Structure_Visualisation (Test #1): passed\n-FROGS_preprocess (Test #1): failed\n-FROGS_preprocess (Test #2): failed\n-FROGS_remove_chimera (Test #1): passed\n-FROGS_taxonomic_affiliation (Test #1): passed\n-FROGS_Tree (Test #1): passed\n-FROGS_tsv_to_biom (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/preprocess.log --- a/test-data/preprocess.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,2187 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpf5nu7q0b/galaxy-dev\n-Clonage dans \'/tmp/tmpf5nu7q0b/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/.local/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/envs/frogsfunc@4.1.0/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (23.0.1)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.40.0)\n-\n-[notice] A new release of pip is available: 23.0.1 -> 23.1.2\n-[notice] To update, run: pip install --upgrade pip\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirement'..b'770-4665-adca-3be38edd13ce.dat\' --R1-size 267 --R2-size 266 --mismatch-rate 0.15 --merge-software vsearch --keep-unmerged]\n-galaxy.jobs.runners DEBUG 2023-05-19 19:24:28,921 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] (4) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpf5nu7q0b/job_working_directory/000/4/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpf5nu7q0b/job_working_directory/000/4/galaxy_4.ec; \n-if [ -f "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/dereplicated.fasta" ] ; then cp "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/dereplicated.fasta" "/tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_e2c97707-a166-4579-98d6-4bf7516ad47e.dat" ; fi; \n-if [ -f "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/count.tsv" ] ; then cp "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/count.tsv" "/tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_bb215308-43aa-40e3-8098-0818c25d88ab.dat" ; fi; \n-if [ -f "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/report.html" ] ; then cp "/tmp/tmpf5nu7q0b/job_working_directory/000/4/working/report.html" "/tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_670e9a4e-8a70-45a7-94f7-638ffe0f2430.dat" ; fi; cd \'/tmp/tmpf5nu7q0b/job_working_directory/000/4\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-19 19:24:28,943 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] (4) executing job script: /tmp/tmpf5nu7q0b/job_working_directory/000/4/galaxy_4.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-19 19:25:08,489 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 370281\n-galaxy.jobs.runners.local DEBUG 2023-05-19 19:25:08,489 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmpf5nu7q0b/job_working_directory/000/4/galaxy_4.sh\n-galaxy.jobs DEBUG 2023-05-19 19:25:08,529 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_e2c97707-a166-4579-98d6-4bf7516ad47e.dat to /tmp/tmpf5nu7q0b/files/e/2/c/dataset_e2c97707-a166-4579-98d6-4bf7516ad47e.dat\n-galaxy.jobs DEBUG 2023-05-19 19:25:08,529 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_bb215308-43aa-40e3-8098-0818c25d88ab.dat to /tmp/tmpf5nu7q0b/files/b/b/2/dataset_bb215308-43aa-40e3-8098-0818c25d88ab.dat\n-galaxy.jobs DEBUG 2023-05-19 19:25:08,529 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmpf5nu7q0b/job_working_directory/000/4/outputs/galaxy_dataset_670e9a4e-8a70-45a7-94f7-638ffe0f2430.dat to /tmp/tmpf5nu7q0b/files/6/7/0/dataset_670e9a4e-8a70-45a7-94f7-638ffe0f2430.dat\n-galaxy.model.metadata DEBUG 2023-05-19 19:25:08,606 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 6\n-galaxy.model.metadata DEBUG 2023-05-19 19:25:08,638 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 7\n-galaxy.model.metadata DEBUG 2023-05-19 19:25:08,647 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 8\n-galaxy.jobs DEBUG 2023-05-19 19:25:08,726 [pN:main.1,p:369901,tN:LocalRunner.work_thread-2] job_wrapper.finish for job 4 executed (203.612 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 2 test(s) executed passed.\n-FROGS_preprocess (Test #1): passed\n-FROGS_preprocess (Test #2): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/taxo_affi.log --- a/test-data/taxo_affi.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1935 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpv9ahn2ok/galaxy-dev\n-Clonage dans \'/tmp/tmpv9ahn2ok/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (23.0.1)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.40.0)\n-\n-[notice] A new release of pip is available: 23.0.1 -> 23.1.2\n-[notice] To update, run: pip install --upgrade pip\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 9)) ('..b'Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-2048}/1024)) && taxonomic_affiliation.py --reference \'/home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/test-data/databases/frogs_db_data/ITS1.rdp.fasta\' --taxonomy-ranks Domain Phylum Class Order Family Genus Species --input-biom \'/tmp/tmpv9ahn2ok/files/2/7/9/dataset_27937c9c-1fbc-477a-b099-678abaa23667.dat\' --input-fasta \'/tmp/tmpv9ahn2ok/files/1/4/5/dataset_1455887e-4ae8-421d-a28e-a933c5982219.dat\' --output-biom \'/tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_7b0c8ce1-2f28-4ed6-962f-312e182b344d.dat\' --summary \'/tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_e29b56ae-b50b-400d-ade8-e98564b2a375.dat\' --nb-cpus ${GALAXY_SLOTS:-1} --java-mem $GALAXY_MEMORY_GB --rdp]\n-\n-galaxy.jobs.runners DEBUG 2023-05-19 15:13:17,335 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] (3) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpv9ahn2ok/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpv9ahn2ok/job_working_directory/000/3/galaxy_3.ec; \n-if [ -f "/tmp/tmpv9ahn2ok/job_working_directory/000/3/working/affiliation.biom" ] ; then cp "/tmp/tmpv9ahn2ok/job_working_directory/000/3/working/affiliation.biom" "/tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_7b0c8ce1-2f28-4ed6-962f-312e182b344d.dat" ; fi; \n-if [ -f "/tmp/tmpv9ahn2ok/job_working_directory/000/3/working/report.html" ] ; then cp "/tmp/tmpv9ahn2ok/job_working_directory/000/3/working/report.html" "/tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_e29b56ae-b50b-400d-ade8-e98564b2a375.dat" ; fi; cd \'/tmp/tmpv9ahn2ok/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-19 15:13:17,349 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] (3) executing job script: /tmp/tmpv9ahn2ok/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-19 15:13:23,160 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 283405\n-galaxy.jobs.runners.local DEBUG 2023-05-19 15:13:23,162 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpv9ahn2ok/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs DEBUG 2023-05-19 15:13:23,246 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_7b0c8ce1-2f28-4ed6-962f-312e182b344d.dat to /tmp/tmpv9ahn2ok/files/7/b/0/dataset_7b0c8ce1-2f28-4ed6-962f-312e182b344d.dat\n-galaxy.jobs DEBUG 2023-05-19 15:13:23,246 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpv9ahn2ok/job_working_directory/000/3/outputs/galaxy_dataset_e29b56ae-b50b-400d-ade8-e98564b2a375.dat to /tmp/tmpv9ahn2ok/files/e/2/9/dataset_e29b56ae-b50b-400d-ade8-e98564b2a375.dat\n-galaxy.model.metadata DEBUG 2023-05-19 15:13:23,399 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.model.metadata DEBUG 2023-05-19 15:13:23,437 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 4\n-galaxy.jobs DEBUG 2023-05-19 15:13:23,561 [pN:main.1,p:283314,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 3 executed (345.756 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_taxonomic_affiliation (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/taxo_enrichment.tsv --- a/test-data/taxo_enrichment.tsv Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,271 +0,0 @@\n-Taxonomic_rank\tDESeq2_Log2fc_sens\tTaxonomic_name\tNb_total_clusters\tNb_observ_taxonomic_name_from_total\tNb_Deseq2_differentially_abundant(OVER_or_UNDER)\tNb_observ_taxonomic_names_from_diff_abundant\tRatio_between_total_and_diff_abundant\tPvalue\tPadj\tSignificance\n-Kingdom\tunder\tBacteria\t1053\t1052\t446\t446\t1.0009505703422052\t1.0\t1.1894273127753303\t \n-Kingdom\tover\tBacteria\t1053\t1052\t539\t538\t0.9990935191912922\t1.0\t1.1894273127753303\t \n-Kingdom\tover\tArchaea\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Phylum\tunder\tFirmicutes\t1053\t924\t446\t438\t1.1191689476442839\t0.16857521467058206\t0.722465205731066\t \n-Phylum\tunder\tActinobacteriota\t1053\t17\t446\t2\t0.2777631231864943\t0.07791272826318164\t0.5685523413799741\t \n-Phylum\tunder\tProteobacteria\t1053\t19\t446\t6\t0.7455746990795374\t0.6612319979689567\t1.075497828021797\t \n-Phylum\tover\tBacteroidota\t1053\t63\t539\t60\t1.860588391200636\t0.0011351669261284913\t0.029190006671875494\t*\n-Phylum\tover\tFirmicutes\t1053\t924\t539\t424\t0.8964653157603065\t0.16781086719530242\t0.7307892603666395\t \n-Phylum\tover\tCampylobacterota\t1053\t4\t539\t4\t1.9536178107606679\t0.45541696874088\t0.956907249494456\t \n-Phylum\tover\tActinobacteriota\t1053\t17\t539\t15\t1.7237804212594128\t0.13405213838570162\t0.6765248105446624\t \n-Phylum\tover\tCyanobacteria\t1053\t11\t539\t11\t1.9536178107606679\t0.118258108369516\t0.6385937851953863\t \n-Phylum\tover\tDesulfobacterota\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n-Phylum\tover\tProteobacteria\t1053\t19\t539\t11\t1.1310418904403867\t0.8459115632544228\t1.2480662408671812\t \n-Phylum\tover\tEuryarchaeota\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Phylum\tover\tVerrucomicrobiota\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n-Phylum\tover\tFusobacteriota\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Phylum\tover\tSpirochaetota\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Phylum\tover\tPatescibacteria\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n-Phylum\tover\tElusimicrobiota\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Phylum\tover\tDeferribacterota\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Class\tunder\tClostridia\t1053\t809\t446\t376\t1.0973188401780418\t0.2732172729268453\t0.8106446559367938\t \n-Class\tunder\tCoriobacteriia\t1053\t16\t446\t2\t0.2951233183856502\t0.11717288255667199\t0.6660353324273988\t \n-Class\tunder\tBacilli\t1053\t99\t446\t62\t1.4785976355483081\t0.024469955011065025\t0.3003130842267071\t \n-Class\tunder\tGammaproteobacteria\t1053\t15\t446\t6\t0.9443946188340807\t1.0\t1.1894273127753303\t \n-Class\tover\tBacteroidia\t1053\t63\t539\t60\t1.860588391200636\t0.0011351669261284913\t0.029190006671875494\t*\n-Class\tover\tClostridia\t1053\t809\t539\t377\t0.9104003889453298\t0.25364720652701717\t0.7694915254190409\t \n-Class\tover\tCampylobacteria\t1053\t4\t539\t4\t1.9536178107606679\t0.45541696874088\t0.956907249494456\t \n-Class\tover\tCoriobacteriia\t1053\t16\t539\t14\t1.7094155844155845\t0.17287093235368073\t0.7236457633409892\t \n-Class\tover\tVampirivibrionia\t1053\t11\t539\t11\t1.9536178107606679\t0.118258108369516\t0.6385937851953863\t \n-Class\tover\tDesulfovibrionia\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n-Class\tover\tBacilli\t1053\t99\t539\t31\t0.6117389104402091\t0.019927328662647383\t0.25620851137689493\t \n-Class\tover\tGammaproteobacteria\t1053\t15\t539\t7\t0.9116883116883117\t1.0\t1.1894273127753303\t \n-Class\tover\tNegativicutes\t1053\t16\t539\t16\t1.9536178107606679\t0.0616223676700078\t0.4893540962030031\t \n-Class\tover\tAlphaproteobacteria\t1053\t4\t539\t4\t1.9536178107606679\t0.45541696874088\t0.956907249494456\t \n-Class\tover\tMethanobacteria\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Class\tover\tLentisphaeria\t1053\t2\t539\t2\t1.9536178107606679\t0.6080045456777096\t1.0489535292842274\t \n-Class\tover\tFusobacteriia\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Class\tover\tSpirochaetia\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Class\tover\tActinobacteria\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-C'..b'303\t \n-Genus\tover\tMonoglobus\t1053\t14\t539\t6\t0.8372647760402863\t0.8156053043522413\t1.2302426378497495\t \n-Genus\tover\tDefluviitaleaceae UCG-011\t1053\t2\t539\t2\t1.9536178107606679\t0.6080045456777096\t1.0489535292842274\t \n-Genus\tover\tFrisingicoccus\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tSlackia\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n-Genus\tover\tCandidatus Saccharimonas\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tRomboutsia\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\t[Eubacterium] brachy group\t1053\t2\t539\t2\t1.9536178107606679\t0.6080045456777096\t1.0489535292842274\t \n-Genus\tover\tPaludicola\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tRikenella\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tAnaerofustis\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tRuminiclostridium\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tLachnospiraceae NK4A136 group\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n-Genus\tover\tRuminococcus\t1053\t4\t539\t4\t1.9536178107606679\t0.45541696874088\t0.956907249494456\t \n-Genus\tover\tOscillospira\t1053\t2\t539\t2\t1.9536178107606679\t0.6080045456777096\t1.0489535292842274\t \n-Genus\tover\tLachnospiraceae FCS020 group\t1053\t4\t539\t1\t0.48840445269016697\t0.6679746014045207\t1.0767351783834065\t \n-Genus\tover\tSubdoligranulum\t1053\t22\t539\t9\t0.7992072862202733\t0.7024005437634327\t1.1090534901527886\t \n-Genus\tover\tAnaerobiospirillum\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tShuttleworthia\t1053\t3\t539\t3\t1.9536178107606679\t0.41388704630371953\t0.9759781877904303\t \n-Genus\tover\tUC5-1-2E3\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tEisenbergiella\t1053\t9\t539\t3\t0.6512059369202227\t0.7607987197842374\t1.1771670735916568\t \n-Genus\tover\tEnorma\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tHoldemania\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tUCG-007\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tVerruc-01\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tMailhella\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tV9D2013 group\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tCollinsella\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tStreptococcus\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tIntestinimonas\t1053\t4\t539\t3\t1.465213358070501\t0.6948956697811112\t1.1069134562884957\t \n-Genus\tover\tUCG-009\t1053\t3\t539\t1\t0.6512059369202227\t1.0\t1.1894273127753303\t \n-Genus\tover\tButyricimonas\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tAnaerofilum\t1053\t7\t539\t1\t0.2790882586800954\t0.27940399260505516\t0.8155576000363772\t \n-Genus\tover\tPseudoflavonifractor\t1053\t11\t539\t1\t0.17760161916006073\t0.07043883619246838\t0.5433853077704703\t \n-Genus\tover\tButyricicoccus\t1053\t32\t539\t2\t0.12210111317254174\t0.00029765878402967713\t0.016073574337602564\t*\n-Genus\tover\t[Eubacterium] ventriosum group\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tFlavonifractor\t1053\t10\t539\t1\t0.1953617810760668\t0.1115103878662504\t0.6690623271975024\t \n-Genus\tover\tEndomicrobium\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tFournierella\t1053\t7\t539\t1\t0.2790882586800954\t0.27940399260505516\t0.8155576000363772\t \n-Genus\tover\tPrevotellaceae UCG-001\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tNegativibacillus\t1053\t4\t539\t1\t0.48840445269016697\t0.6679746014045207\t1.0767351783834065\t \n-Genus\tover\tHelicobacter\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tCoprococcus\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tMerdibacter\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n-Genus\tover\tMucispirillum\t1053\t1\t539\t1\t1.9536178107606679\t1.0\t1.1894273127753303\t \n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/taxonomic_affiliation.log --- a/test-data/taxonomic_affiliation.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,4322 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp8zb9uvoe/galaxy-dev\n-Clonage dans \'/tmp/tmp8zb9uvoe/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'-dev/lib/galaxy/jobs/command_factory.py", line 81, in build_command\n- __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n- File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n- if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n- File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n- self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n- File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n- return self.app.toolbox.dependency_manager.dependency_shell_commands(\n- File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n- self.build_cache(requirements, **kwds)\n- File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n- self.build_environment()\n- File "/tmp/tmp7b_u0d84/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n- raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n-galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n-galaxy.jobs DEBUG 2023-04-25 09:01:44,478 [pN:main.1,p:115722,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp7b_u0d84/job_working_directory/000/3/outputs/galaxy_dataset_8699930c-0294-4403-a908-5f848a23c91a.dat to /tmp/tmp7b_u0d84/files/8/6/9/dataset_8699930c-0294-4403-a908-5f848a23c91a.dat\n-galaxy.jobs DEBUG 2023-04-25 09:01:44,479 [pN:main.1,p:115722,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmp7b_u0d84/job_working_directory/000/3/outputs/galaxy_dataset_e879ac4e-3717-4720-94c4-4d80c890ec87.dat to /tmp/tmp7b_u0d84/files/e/8/7/dataset_e879ac4e-3717-4720-94c4-4d80c890ec87.dat\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_taxonomic_affiliation (Test #1): failed\n-Traceback (most recent call last):\n- File "/home/vdarbot/.local/bin/planemo", line 5, in <module>\n- from planemo.cli import planemo\n-ModuleNotFoundError: No module named \'planemo\'\n-Traceback (most recent call last):\n- File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/bin/planemo", line 6, in <module>\n- from planemo.cli import planemo\n- File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/planemo/cli.py", line 14, in <module>\n- from planemo.galaxy import profiles\n- File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/planemo/galaxy/__init__.py", line 4, in <module>\n- from .config import galaxy_config\n- File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/planemo/galaxy/config.py", line 25, in <module>\n- from planemo.galaxy.workflows import remote_runnable_to_workflow_id\n- File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/planemo/galaxy/workflows.py", line 14, in <module>\n- from ephemeris import (\n- File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/ephemeris/generate_tool_list_from_ga_workflow_files.py", line 13, in <module>\n- from .shed_tools import InstallRepoDict\n- File "/home/vdarbot/miniconda3/envs/__frogs@4.1.0/lib/python3.6/site-packages/ephemeris/shed_tools.py", line 62, in <module>\n- from typing_extensions import (\n-ImportError: cannot import name \'NamedTuple\'\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/test/deseq2_preprocess.log --- a/test-data/test/deseq2_preprocess.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,6538 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp833m4nfr/galaxy-dev\n-Clonage dans \'/tmp/tmp833m4nfr/galaxy-dev\'...\n-fait.\n-Mise \xc3\xa0 jour des fichiers: 60% (3720/6176)\rMise \xc3\xa0 jour des fichiers: 61% (3768/6176)\rMise \xc3\xa0 jour des fichiers: 62% (3830/6176)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6176)\rMise \xc3\xa0 jour des fichiers: 64% (3953/6176)\rMise \xc3\xa0 jour des fichiers: 65% (4015/6176)\rMise \xc3\xa0 jour des fichiers: 66% (4077/6176)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6176)\rMise \xc3\xa0 jour des fichiers: 68% (4200/6176)\rMise \xc3\xa0 jour des fichiers: 69% (4262/6176)\rMise \xc3\xa0 jour des fichiers: 70% (4324/6176)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6176)\rMise \xc3\xa0 jour des fichiers: 72% (4447/6176)\rMise \xc3\xa0 jour des fichiers: 73% (4509/6176)\rMise \xc3\xa0 jour des fichiers: 74% (4571/6176)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6176)\rMise \xc3\xa0 jour des fichiers: 76% (4694/6176)\rMise \xc3\xa0 jour des fichiers: 77% (4756/6176)\rMise \xc3\xa0 jour des fichiers: 78% (4818/6176)\rMise \xc3\xa0 jour des fichiers: 79% (4880/6176)\rMise \xc3\xa0 jour des fichiers: 80% (4941/6176)\rMise \xc3\xa0 jour des fichiers: 81% (5003/6176)\rMise \xc3\xa0 jour des fichiers: 82% (5065/6176)\rMise \xc3\xa0 jour des fichiers: 83% (5127/6176)\rMise \xc3\xa0 jour des fichiers: 84% (5188/6176)\rMise \xc3\xa0 jour des fichiers: 85% (5250/6176)\rMise \xc3\xa0 jour des fichiers: 86% (5312/6176)\rMise \xc3\xa0 jour des fichiers: 87% (5374/6176)\rMise \xc3\xa0 jour des fichiers: 88% (5435/6176)\rMise \xc3\xa0 jour des fichiers: 89% (5497/6176)\rMise \xc3\xa0 jour des fichiers: 90% (5559/6176)\rMise \xc3\xa0 jour des fichiers: 91% (5621/6176)\rMise \xc3\xa0 jour des fichiers: 92% (5682/6176)\rMise \xc3\xa0 jour des fichiers: 93% (5744/6176)\rMise \xc3\xa0 jour des fichiers: 94% (5806/6176)\rMise \xc3\xa0 jour des fichiers: 95% (5868/6176)\rMise \xc3\xa0 jour des fichiers: 96% (5929/6176)\rMise \xc3\xa0 jour des fichiers: 97% (5991/6176)\rMise \xc3\xa0 jour des fichiers: 98% (6053/6176)\rMise \xc3\xa0 jour des fichiers: 99% (6115/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176), fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: ma'..b'3b865de29fe8f6184\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-0e77690e926ae6fbe6e97e77dd7669e3223fe1b06ce28fe3b865de29fe8f6184\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; deseq2_preprocess.py --analysis \'ASV\' --data \'/tmp/tmpvxp3pnmm/files/9/6/5/dataset_9652a7ff-5a94-4a05-8bfb-5d14a84addfa.dat\' --out-Rdata \'/tmp/tmpvxp3pnmm/job_working_directory/000/2/outputs/galaxy_dataset_b36f895f-38be-49a4-a342-4c975571abee.dat\' --var \'EnvType\']\n-galaxy.jobs.runners DEBUG 2023-05-09 09:29:06,375 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpvxp3pnmm/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpvxp3pnmm/job_working_directory/000/2/galaxy_2.ec; \n-if [ -f "/tmp/tmpvxp3pnmm/job_working_directory/000/2/working/asv_dds.Rdata" ] ; then cp "/tmp/tmpvxp3pnmm/job_working_directory/000/2/working/asv_dds.Rdata" "/tmp/tmpvxp3pnmm/job_working_directory/000/2/outputs/galaxy_dataset_b36f895f-38be-49a4-a342-4c975571abee.dat" ; fi; cd \'/tmp/tmpvxp3pnmm/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-09 09:29:06,412 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] (2) executing job script: /tmp/tmpvxp3pnmm/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 09:29:10,718 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 33253\n-galaxy.jobs.runners.local DEBUG 2023-05-09 09:29:10,718 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpvxp3pnmm/job_working_directory/000/2/galaxy_2.sh\n-galaxy.tool_util.output_checker INFO 2023-05-09 09:29:10,723 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] Job error detected, failing job. Reasons are [{\'type\': \'exit_code\', \'desc\': \'Fatal error: Exit code 127 ()\', \'exit_code\': 127, \'code_desc\': \'\', \'error_level\': 3}]\n-galaxy.jobs DEBUG 2023-05-09 09:29:10,748 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpvxp3pnmm/job_working_directory/000/2/outputs/galaxy_dataset_b36f895f-38be-49a4-a342-4c975571abee.dat to /tmp/tmpvxp3pnmm/files/b/3/6/dataset_b36f895f-38be-49a4-a342-4c975571abee.dat\n-galaxy.jobs DEBUG 2023-05-09 09:29:10,846 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] (2) setting dataset 2 state to ERROR\n-galaxy.jobs DEBUG 2023-05-09 09:29:10,992 [pN:main.1,p:33198,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 2 executed (251.730 ms)\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGSSTAT_DESeq2_Preprocess (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/test/frogsfunc_function.log --- a/test-data/test/frogsfunc_function.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1438 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmppl8bdhp8/galaxy-dev\n-Clonage dans \'/tmp/tmppl8bdhp8/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (23.0.1)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.40.0)\n-\n-[notice] A new release of pip is available: 23.0.1 -> 23.1.2\n-[notice] To update, run: pip install --upgrade pip\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 9)) ('..b'ctory.py", line 81, in build_command\n- __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)\n- File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/jobs/command_factory.py", line 234, in __handle_dependency_resolution\n- if local_dependency_resolution and job_wrapper.dependency_shell_commands:\n- File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1107, in dependency_shell_commands\n- self._dependency_shell_commands = self.tool.build_dependency_shell_commands(\n- File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tools/__init__.py", line 2069, in build_dependency_shell_commands\n- return self.app.toolbox.dependency_manager.dependency_shell_commands(\n- File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 420, in dependency_shell_commands\n- self.build_cache(requirements, **kwds)\n- File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in build_cache\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tool_util/deps/__init__.py", line 405, in <listcomp>\n- [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]\n- File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 484, in build_cache\n- self.build_environment()\n- File "/tmp/tmppl8bdhp8/galaxy-dev/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment\n- raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")\n-galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.\n-galaxy.jobs DEBUG 2023-05-19 16:04:04,194 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_bb3e7f6f-d9c9-4d3c-b660-bc2929f6a46d.dat to /tmp/tmppl8bdhp8/files/b/b/3/dataset_bb3e7f6f-d9c9-4d3c-b660-bc2929f6a46d.dat\n-galaxy.jobs DEBUG 2023-05-19 16:04:04,196 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_99793432-3096-457e-981e-6c01776f985c.dat to /tmp/tmppl8bdhp8/files/9/9/7/dataset_99793432-3096-457e-981e-6c01776f985c.dat\n-galaxy.jobs DEBUG 2023-05-19 16:04:04,197 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_f64e4735-b301-4f8d-a533-b023e9c931ff.dat to /tmp/tmppl8bdhp8/files/f/6/4/dataset_f64e4735-b301-4f8d-a533-b023e9c931ff.dat\n-galaxy.jobs DEBUG 2023-05-19 16:04:04,198 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_9530a299-a956-452f-9dc4-64a85af59daf.dat to /tmp/tmppl8bdhp8/files/9/5/3/dataset_9530a299-a956-452f-9dc4-64a85af59daf.dat\n-galaxy.jobs DEBUG 2023-05-19 16:04:04,200 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_1c6b2c69-d5eb-4ea9-b577-646a5cf03b7c.dat to /tmp/tmppl8bdhp8/files/1/c/6/dataset_1c6b2c69-d5eb-4ea9-b577-646a5cf03b7c.dat\n-galaxy.jobs DEBUG 2023-05-19 16:04:04,201 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_b5ad6f82-05b9-4346-9e4e-cca9bb0e76c6.dat to /tmp/tmppl8bdhp8/files/b/5/a/dataset_b5ad6f82-05b9-4346-9e4e-cca9bb0e76c6.dat\n-galaxy.jobs DEBUG 2023-05-19 16:04:04,202 [pN:main.1,p:317899,tN:LocalRunner.work_thread-0] fail(): Moved /tmp/tmppl8bdhp8/job_working_directory/000/3/outputs/galaxy_dataset_4c101ec2-bcd1-444b-ba28-6f52686c0009.dat to /tmp/tmppl8bdhp8/files/4/c/1/dataset_4c101ec2-bcd1-444b-ba28-6f52686c0009.dat\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGSFUNC_step1_placeseqs (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/test/frogsfunc_pathway.log --- a/test-data/test/frogsfunc_pathway.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1058 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp13l64xd9/galaxy-dev\n-Clonage dans \'/tmp/tmp13l64xd9/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'iconda3/envs/mulled-v1-0ba21a4ae58f6e1dad373d217531ef4f6cd0ce45cfa2892e499f6ac681126382\')" ] || {\n-MAX_TRIES=3\n-COUNT=0\n-while [ $COUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-0ba21a4ae58f6e1dad373d217531ef4f6cd0ce45cfa2892e499f6ac681126382\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; frogsfunc_pathways.py --input-file /tmp/tmp13l64xd9/files/5/a/5/dataset_5a556338-76d1-4220-9780-158113435cca.dat --map /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/test-data/databases/frogs_picrust2_db/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt --summary /tmp/tmp13l64xd9/job_working_directory/000/2/outputs/galaxy_dataset_352c1def-fa51-4411-8e60-c5641dc4dc2d.dat]\n-galaxy.jobs.runners DEBUG 2023-05-09 11:56:47,840 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmp13l64xd9/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp13l64xd9/job_working_directory/000/2/galaxy_2.ec; \n-if [ -f "/tmp/tmp13l64xd9/job_working_directory/000/2/working/report.html" ] ; then cp "/tmp/tmp13l64xd9/job_working_directory/000/2/working/report.html" "/tmp/tmp13l64xd9/job_working_directory/000/2/outputs/galaxy_dataset_352c1def-fa51-4411-8e60-c5641dc4dc2d.dat" ; fi; \n-if [ -f "/tmp/tmp13l64xd9/job_working_directory/000/2/working/frogsfunc_pathways_unstrat.tsv" ] ; then cp "/tmp/tmp13l64xd9/job_working_directory/000/2/working/frogsfunc_pathways_unstrat.tsv" "/tmp/tmp13l64xd9/job_working_directory/000/2/outputs/galaxy_dataset_7ffd4c72-ac4d-44c8-8707-22a80707e74d.dat" ; fi; cd \'/tmp/tmp13l64xd9/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-09 11:56:47,856 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] (2) executing job script: /tmp/tmp13l64xd9/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 11:57:58,456 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 58241\n-galaxy.jobs.runners.local DEBUG 2023-05-09 11:57:58,456 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmp13l64xd9/job_working_directory/000/2/galaxy_2.sh\n-galaxy.jobs DEBUG 2023-05-09 11:57:58,489 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmp13l64xd9/job_working_directory/000/2/outputs/galaxy_dataset_352c1def-fa51-4411-8e60-c5641dc4dc2d.dat to /tmp/tmp13l64xd9/files/3/5/2/dataset_352c1def-fa51-4411-8e60-c5641dc4dc2d.dat\n-galaxy.jobs DEBUG 2023-05-09 11:57:58,489 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmp13l64xd9/job_working_directory/000/2/outputs/galaxy_dataset_7ffd4c72-ac4d-44c8-8707-22a80707e74d.dat to /tmp/tmp13l64xd9/files/7/f/f/dataset_7ffd4c72-ac4d-44c8-8707-22a80707e74d.dat\n-galaxy.model.metadata DEBUG 2023-05-09 11:57:58,561 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 2\n-galaxy.model.metadata DEBUG 2023-05-09 11:57:58,581 [pN:main.1,p:58187,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 3\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGSFUNC_step4_pathways (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/test/frogsfunc_pathways.log --- a/test-data/test/frogsfunc_pathways.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1910 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpbjte8_kh/galaxy-dev\n-Clonage dans \'/tmp/tmpbjte8_kh/galaxy-dev\'...\n-fait.\n-Mise \xc3\xa0 jour des fichiers: 47% (2961/6177)\rMise \xc3\xa0 jour des fichiers: 48% (2965/6177)\rMise \xc3\xa0 jour des fichiers: 49% (3027/6177)\rMise \xc3\xa0 jour des fichiers: 50% (3089/6177)\rMise \xc3\xa0 jour des fichiers: 51% (3151/6177)\rMise \xc3\xa0 jour des fichiers: 52% (3213/6177)\rMise \xc3\xa0 jour des fichiers: 53% (3274/6177)\rMise \xc3\xa0 jour des fichiers: 54% (3336/6177)\rMise \xc3\xa0 jour des fichiers: 55% (3398/6177)\rMise \xc3\xa0 jour des fichiers: 56% (3460/6177)\rMise \xc3\xa0 jour des fichiers: 57% (3521/6177)\rMise \xc3\xa0 jour des fichiers: 58% (3583/6177)\rMise \xc3\xa0 jour des fichiers: 59% (3645/6177)\rMise \xc3\xa0 jour des fichiers: 60% (3707/6177)\rMise \xc3\xa0 jour des fichiers: 61% (3768/6177)\rMise \xc3\xa0 jour des fichiers: 62% (3830/6177)\rMise \xc3\xa0 jour des fichiers: 63% (3892/6177)\rMise \xc3\xa0 jour des fichiers: 64% (3954/6177)\rMise \xc3\xa0 jour des fichiers: 65% (4016/6177)\rMise \xc3\xa0 jour des fichiers: 66% (4077/6177)\rMise \xc3\xa0 jour des fichiers: 67% (4139/6177)\rMise \xc3\xa0 jour des fichiers: 68% (4201/6177)\rMise \xc3\xa0 jour des fichiers: 69% (4263/6177)\rMise \xc3\xa0 jour des fichiers: 70% (4324/6177)\rMise \xc3\xa0 jour des fichiers: 71% (4386/6177)\rMise \xc3\xa0 jour des fichiers: 72% (4448/6177)\rMise \xc3\xa0 jour des fichiers: 73% (4510/6177)\rMise \xc3\xa0 jour des fichiers: 74% (4571/6177)\rMise \xc3\xa0 jour des fichiers: 75% (4633/6177)\rMise \xc3\xa0 jour des fichiers: 76% (4695/6177)\rMise \xc3\xa0 jour des fichiers: 77% (4757/6177)\rMise \xc3\xa0 jour des fichiers: 78% (4819/6177)\rMise \xc3\xa0 jour des fichiers: 79% (4880/6177)\rMise \xc3\xa0 jour des fichiers: 80% (4942/6177)\rMise \xc3\xa0 jour des fichiers: 81% (5004/6177)\rMise \xc3\xa0 jour des fichiers: 82% (5066/6177)\rMise \xc3\xa0 jour des fichiers: 83% (5127/6177)\rMise \xc3\xa0 jour des fichiers: 84% (5189/6177)\rMise \xc3\xa0 jour des fichiers: 85% (5251/6177)\rMise \xc3\xa0 jour des fichiers: 86% (5313/6177)\rMise \xc3\xa0 jour des fichiers: 87% (5374/6177)\rMise \xc3\xa0 jour des fichiers: 88% (5436/6177)\rMise \xc3\xa0 jour des fichiers: 89% (5498/6177)\rMise \xc3\xa0 jour des fichiers: 90% (5560/6177)\rMise \xc3\xa0 jour des fichiers: 91% (5622/6177)\rMise \xc3\xa0 jour des fichiers: 92% (5683/6177)\rMise \xc3\xa0 jour des fichiers: 93% (5745/6177)\rMise \xc3\xa0 jour des fichiers: 94% (5807/6177)\rMise \xc3\xa0 jour des fichiers: 95% (5869/6177)\rMise \xc3\xa0 jour des fichiers: 96% (5930/6177)\rMise \xc3\xa0 jour des fichiers: 97% (5992/6177)\rMise \xc3\xa0 jour des fichiers: 98% (6054/6177)\rMise \xc3\xa0 jour des fichiers: 99% (6116/6177)\rMise \xc3\xa0 jour des fichiers: 100% (6177/6177)\rMise \xc3\xa0 jour des fichiers: 100% (6177/6177), fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement alr'..b'MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; frogsfunc_pathways.py --input-file /tmp/tmpbjte8_kh/files/e/5/d/dataset_e5dac98d-9aff-4195-bdff-9aff88e1def9.dat --map /home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/test-data/databases/frogs_picrust2_db/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt --summary /tmp/tmpbjte8_kh/job_working_directory/000/2/outputs/galaxy_dataset_75fd79d2-e1a2-4cf6-a728-006bdab8dcd6.dat]\n-galaxy.jobs.runners DEBUG 2023-05-19 16:14:01,505 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpbjte8_kh/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpbjte8_kh/job_working_directory/000/2/galaxy_2.ec; \n-if [ -f "/tmp/tmpbjte8_kh/job_working_directory/000/2/working/report.html" ] ; then cp "/tmp/tmpbjte8_kh/job_working_directory/000/2/working/report.html" "/tmp/tmpbjte8_kh/job_working_directory/000/2/outputs/galaxy_dataset_75fd79d2-e1a2-4cf6-a728-006bdab8dcd6.dat" ; fi; \n-if [ -f "/tmp/tmpbjte8_kh/job_working_directory/000/2/working/frogsfunc_pathways_unstrat.tsv" ] ; then cp "/tmp/tmpbjte8_kh/job_working_directory/000/2/working/frogsfunc_pathways_unstrat.tsv" "/tmp/tmpbjte8_kh/job_working_directory/000/2/outputs/galaxy_dataset_6747e83c-e4f3-4d4c-b0eb-0bda0b685bd2.dat" ; fi; cd \'/tmp/tmpbjte8_kh/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-19 16:14:01,537 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] (2) executing job script: /tmp/tmpbjte8_kh/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-19 16:15:34,372 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 350452\n-galaxy.jobs.runners.local DEBUG 2023-05-19 16:15:34,380 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmpbjte8_kh/job_working_directory/000/2/galaxy_2.sh\n-galaxy.tool_util.output_checker INFO 2023-05-19 16:15:34,404 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] Job error detected, failing job. Reasons are [{\'type\': \'exit_code\', \'desc\': \'Fatal error: Exit code 1 ()\', \'exit_code\': 1, \'code_desc\': \'\', \'error_level\': 3}]\n-galaxy.jobs DEBUG 2023-05-19 16:15:34,502 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpbjte8_kh/job_working_directory/000/2/outputs/galaxy_dataset_75fd79d2-e1a2-4cf6-a728-006bdab8dcd6.dat to /tmp/tmpbjte8_kh/files/7/5/f/dataset_75fd79d2-e1a2-4cf6-a728-006bdab8dcd6.dat\n-galaxy.jobs DEBUG 2023-05-19 16:15:34,510 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmpbjte8_kh/job_working_directory/000/2/outputs/galaxy_dataset_6747e83c-e4f3-4d4c-b0eb-0bda0b685bd2.dat to /tmp/tmpbjte8_kh/files/6/7/4/dataset_6747e83c-e4f3-4d4c-b0eb-0bda0b685bd2.dat\n-galaxy.jobs DEBUG 2023-05-19 16:15:34,756 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] (2) setting dataset 2 state to ERROR\n-galaxy.jobs DEBUG 2023-05-19 16:15:34,772 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] (2) setting dataset 3 state to ERROR\n-galaxy.jobs DEBUG 2023-05-19 16:15:35,182 [pN:main.1,p:350346,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 2 executed (719.836 ms)\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGSFUNC_step4_pathways (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/test/frogsfunc_placeseqs.log --- a/test-data/test/frogsfunc_placeseqs.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,7143 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpnylvbdf7/galaxy-dev\n-Clonage dans \'/tmp/tmpnylvbdf7/galaxy-dev\'...\n-fait.\n-Mise \xc3\xa0 jour des fichiers: 53% (3331/6176)\rMise \xc3\xa0 jour des fichiers: 54% (3336/6176)\rMise \xc3\xa0 jour des fichiers: 55% (3397/6176)\rMise \xc3\xa0 jour des fichiers: 56% (3459/6176)\rMise \xc3\xa0 jour des fichiers: 57% (3521/6176)\rMise \xc3\xa0 jour des fichiers: 58% (3583/6176)\rMise \xc3\xa0 jour des fichiers: 59% (3644/6176)\rMise \xc3\xa0 jour des fichiers: 60% (3706/6176)\rMise \xc3\xa0 jour des fichiers: 61% (3768/6176)\rMise \xc3\xa0 jour des fichiers: 62% (3830/6176)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6176)\rMise \xc3\xa0 jour des fichiers: 64% (3953/6176)\rMise \xc3\xa0 jour des fichiers: 65% (4015/6176)\rMise \xc3\xa0 jour des fichiers: 66% (4077/6176)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6176)\rMise \xc3\xa0 jour des fichiers: 68% (4200/6176)\rMise \xc3\xa0 jour des fichiers: 69% (4262/6176)\rMise \xc3\xa0 jour des fichiers: 70% (4324/6176)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6176)\rMise \xc3\xa0 jour des fichiers: 72% (4447/6176)\rMise \xc3\xa0 jour des fichiers: 73% (4509/6176)\rMise \xc3\xa0 jour des fichiers: 74% (4571/6176)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6176)\rMise \xc3\xa0 jour des fichiers: 76% (4694/6176)\rMise \xc3\xa0 jour des fichiers: 77% (4756/6176)\rMise \xc3\xa0 jour des fichiers: 78% (4818/6176)\rMise \xc3\xa0 jour des fichiers: 79% (4880/6176)\rMise \xc3\xa0 jour des fichiers: 80% (4941/6176)\rMise \xc3\xa0 jour des fichiers: 81% (5003/6176)\rMise \xc3\xa0 jour des fichiers: 82% (5065/6176)\rMise \xc3\xa0 jour des fichiers: 83% (5127/6176)\rMise \xc3\xa0 jour des fichiers: 84% (5188/6176)\rMise \xc3\xa0 jour des fichiers: 85% (5250/6176)\rMise \xc3\xa0 jour des fichiers: 86% (5312/6176)\rMise \xc3\xa0 jour des fichiers: 87% (5374/6176)\rMise \xc3\xa0 jour des fichiers: 88% (5435/6176)\rMise \xc3\xa0 jour des fichiers: 89% (5497/6176)\rMise \xc3\xa0 jour des fichiers: 90% (5559/6176)\rMise \xc3\xa0 jour des fichiers: 91% (5621/6176)\rMise \xc3\xa0 jour des fichiers: 92% (5682/6176)\rMise \xc3\xa0 jour des fichiers: 93% (5744/6176)\rMise \xc3\xa0 jour des fichiers: 94% (5806/6176)\rMise \xc3\xa0 jour des fichiers: 95% (5868/6176)\rMise \xc3\xa0 jour des fichiers: 96% (5929/6176)\rMise \xc3\xa0 jour des fichiers: 97% (5991/6176)\rMise \xc3\xa0 jour des fichiers: 98% (6053/6176)\rMise \xc3\xa0 jour des fichiers: 99% (6115/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176), fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, v'..b'.handler INFO 2023-05-09 12:08:46,918 [pN:main.1,p:59716,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n-galaxy.jobs DEBUG 2023-05-09 12:08:47,030 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] Job wrapper for Job [2] prepared (104.686 ms)\n-galaxy.jobs.command_factory INFO 2023-05-09 12:08:47,047 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] Built script [/tmp/tmpqihjec1x/job_working_directory/000/2/tool_script.sh] for tool command [python \'/tmp/tmpqihjec1x/galaxy-dev/tools/data_source/upload.py\' \'/tmp/tmpqihjec1x/galaxy-dev\' \'/tmp/tmpqihjec1x/job_working_directory/000/2/registry.xml\' \'/tmp/tmpqihjec1x/tmp/upload_params_jmuygh1j\' \'2:/tmp/tmpqihjec1x/job_working_directory/000/2/working/dataset_1c58f0a1-9180-4a1c-a069-2af497d19cc7_files:/tmp/tmpqihjec1x/job_working_directory/000/2/outputs/galaxy_dataset_1c58f0a1-9180-4a1c-a069-2af497d19cc7.dat\']\n-galaxy.jobs.runners DEBUG 2023-05-09 12:08:47,195 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpqihjec1x/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpqihjec1x/job_working_directory/000/2/galaxy_2.ec; cd \'/tmp/tmpqihjec1x/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-09 12:08:47,216 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] (2) executing job script: /tmp/tmpqihjec1x/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 12:08:52,499 [pN:main.1,p:59716,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 59735\n-galaxy.jobs.runners.local DEBUG 2023-05-09 12:08:52,500 [pN:main.1,p:59716,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpqihjec1x/job_working_directory/000/1/galaxy_1.sh\n-galaxy.jobs DEBUG 2023-05-09 12:08:52,569 [pN:main.1,p:59716,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpqihjec1x/job_working_directory/000/1/outputs/galaxy_dataset_1825cf33-e6b6-4ab5-aaec-c075b0ac7d36.dat to /tmp/tmpqihjec1x/files/1/8/2/dataset_1825cf33-e6b6-4ab5-aaec-c075b0ac7d36.dat\n-galaxy.model.metadata DEBUG 2023-05-09 12:08:52,678 [pN:main.1,p:59716,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 1\n-galaxy.jobs DEBUG 2023-05-09 12:08:52,768 [pN:main.1,p:59716,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 1 executed (218.260 ms)\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 12:08:53,940 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] check_pg(): No process found in process group 59756\n-galaxy.jobs.runners.local DEBUG 2023-05-09 12:08:53,940 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] execution finished: /tmp/tmpqihjec1x/job_working_directory/000/2/galaxy_2.sh\n-galaxy.jobs DEBUG 2023-05-09 12:08:53,975 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] finish(): Moved /tmp/tmpqihjec1x/job_working_directory/000/2/outputs/galaxy_dataset_1c58f0a1-9180-4a1c-a069-2af497d19cc7.dat to /tmp/tmpqihjec1x/files/1/c/5/dataset_1c58f0a1-9180-4a1c-a069-2af497d19cc7.dat\n-galaxy.model.metadata DEBUG 2023-05-09 12:08:54,077 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 2\n-galaxy.jobs DEBUG 2023-05-09 12:08:54,186 [pN:main.1,p:59716,tN:LocalRunner.work_thread-2] job_wrapper.finish for job 2 executed (220.424 ms)\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 1 test(s) - out of 1 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGSFUNC_step1_placeseqs (Test #1): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/test/preprocess.log --- a/test-data/test/preprocess.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,2182 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp7qbuuh95/galaxy-dev\n-Clonage dans \'/tmp/tmp7qbuuh95/galaxy-dev\'...\n-fait.\n-Mise \xc3\xa0 jour des fichiers: 45% (2792/6176)\rMise \xc3\xa0 jour des fichiers: 46% (2841/6176)\rMise \xc3\xa0 jour des fichiers: 47% (2903/6176)\rMise \xc3\xa0 jour des fichiers: 48% (2965/6176)\rMise \xc3\xa0 jour des fichiers: 49% (3027/6176)\rMise \xc3\xa0 jour des fichiers: 50% (3088/6176)\rMise \xc3\xa0 jour des fichiers: 51% (3150/6176)\rMise \xc3\xa0 jour des fichiers: 52% (3212/6176)\rMise \xc3\xa0 jour des fichiers: 53% (3274/6176)\rMise \xc3\xa0 jour des fichiers: 54% (3336/6176)\rMise \xc3\xa0 jour des fichiers: 55% (3397/6176)\rMise \xc3\xa0 jour des fichiers: 56% (3459/6176)\rMise \xc3\xa0 jour des fichiers: 57% (3521/6176)\rMise \xc3\xa0 jour des fichiers: 58% (3583/6176)\rMise \xc3\xa0 jour des fichiers: 59% (3644/6176)\rMise \xc3\xa0 jour des fichiers: 60% (3706/6176)\rMise \xc3\xa0 jour des fichiers: 61% (3768/6176)\rMise \xc3\xa0 jour des fichiers: 62% (3830/6176)\rMise \xc3\xa0 jour des fichiers: 63% (3891/6176)\rMise \xc3\xa0 jour des fichiers: 64% (3953/6176)\rMise \xc3\xa0 jour des fichiers: 65% (4015/6176)\rMise \xc3\xa0 jour des fichiers: 66% (4077/6176)\rMise \xc3\xa0 jour des fichiers: 67% (4138/6176)\rMise \xc3\xa0 jour des fichiers: 68% (4200/6176)\rMise \xc3\xa0 jour des fichiers: 69% (4262/6176)\rMise \xc3\xa0 jour des fichiers: 70% (4324/6176)\rMise \xc3\xa0 jour des fichiers: 71% (4385/6176)\rMise \xc3\xa0 jour des fichiers: 72% (4447/6176)\rMise \xc3\xa0 jour des fichiers: 73% (4509/6176)\rMise \xc3\xa0 jour des fichiers: 74% (4571/6176)\rMise \xc3\xa0 jour des fichiers: 75% (4632/6176)\rMise \xc3\xa0 jour des fichiers: 76% (4694/6176)\rMise \xc3\xa0 jour des fichiers: 77% (4756/6176)\rMise \xc3\xa0 jour des fichiers: 78% (4818/6176)\rMise \xc3\xa0 jour des fichiers: 79% (4880/6176)\rMise \xc3\xa0 jour des fichiers: 80% (4941/6176)\rMise \xc3\xa0 jour des fichiers: 81% (5003/6176)\rMise \xc3\xa0 jour des fichiers: 82% (5065/6176)\rMise \xc3\xa0 jour des fichiers: 83% (5127/6176)\rMise \xc3\xa0 jour des fichiers: 84% (5188/6176)\rMise \xc3\xa0 jour des fichiers: 85% (5250/6176)\rMise \xc3\xa0 jour des fichiers: 86% (5312/6176)\rMise \xc3\xa0 jour des fichiers: 87% (5374/6176)\rMise \xc3\xa0 jour des fichiers: 88% (5435/6176)\rMise \xc3\xa0 jour des fichiers: 89% (5497/6176)\rMise \xc3\xa0 jour des fichiers: 90% (5559/6176)\rMise \xc3\xa0 jour des fichiers: 91% (5621/6176)\rMise \xc3\xa0 jour des fichiers: 92% (5682/6176)\rMise \xc3\xa0 jour des fichiers: 93% (5744/6176)\rMise \xc3\xa0 jour des fichiers: 94% (5806/6176)\rMise \xc3\xa0 jour des fichiers: 95% (5868/6176)\rMise \xc3\xa0 jour des fichiers: 96% (5929/6176)\rMise \xc3\xa0 jour des fichiers: 97% (5991/6176)\rMise \xc3\xa0 jour des fichiers: 98% (6053/6176)\rMise \xc3\xa0 jour des fichiers: 99% (6115/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176)\rMise \xc3\xa0 jour des fichiers: 100% (6176/6176), fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome'..b'.1,p:159691,tN:WSGI_0] (Job[id=2,tool_id=upload1]) Handler \'_default_\' assigned using \'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED\' assignment method\n-galaxy.tools.execute DEBUG 2023-05-09 13:05:04,671 [pN:main.1,p:159691,tN:WSGI_0] Created 1 job(s) for tool upload1 request (190.789 ms)\n-galaxy.jobs.mapper DEBUG 2023-05-09 13:05:04,940 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: upload_dest\n-galaxy.jobs.handler DEBUG 2023-05-09 13:05:04,949 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to planemo_runner runner\n-galaxy.jobs DEBUG 2023-05-09 13:05:05,010 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: upload_dest)\n-galaxy.jobs DEBUG 2023-05-09 13:05:05,020 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /tmp/tmpkmhzemjv/job_working_directory/000/2\n-galaxy.jobs.runners DEBUG 2023-05-09 13:05:05,046 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] Job [2] queued (97.041 ms)\n-galaxy.jobs.handler INFO 2023-05-09 13:05:05,057 [pN:main.1,p:159691,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched\n-galaxy.jobs DEBUG 2023-05-09 13:05:05,185 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] Job wrapper for Job [2] prepared (93.411 ms)\n-galaxy.jobs.command_factory INFO 2023-05-09 13:05:05,199 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] Built script [/tmp/tmpkmhzemjv/job_working_directory/000/2/tool_script.sh] for tool command [python \'/tmp/tmpkmhzemjv/galaxy-dev/tools/data_source/upload.py\' \'/tmp/tmpkmhzemjv/galaxy-dev\' \'/tmp/tmpkmhzemjv/job_working_directory/000/2/registry.xml\' \'/tmp/tmpkmhzemjv/tmp/upload_params_0b03oqzh\' \'2:/tmp/tmpkmhzemjv/job_working_directory/000/2/working/dataset_e02e3022-5cb8-4a1a-837b-97a74809bd36_files:/tmp/tmpkmhzemjv/job_working_directory/000/2/outputs/galaxy_dataset_e02e3022-5cb8-4a1a-837b-97a74809bd36.dat\']\n-galaxy.jobs.runners DEBUG 2023-05-09 13:05:05,251 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] (2) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmpkmhzemjv/job_working_directory/000/2/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmpkmhzemjv/job_working_directory/000/2/galaxy_2.ec; cd \'/tmp/tmpkmhzemjv/job_working_directory/000/2\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-09 13:05:05,272 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] (2) executing job script: /tmp/tmpkmhzemjv/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 13:05:09,889 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 159745\n-galaxy.jobs.runners.local DEBUG 2023-05-09 13:05:09,890 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmpkmhzemjv/job_working_directory/000/2/galaxy_2.sh\n-\n-galaxy.jobs DEBUG 2023-05-09 13:05:12,440 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmpkmhzemjv/job_working_directory/000/2/outputs/galaxy_dataset_e02e3022-5cb8-4a1a-837b-97a74809bd36.dat to /tmp/tmpkmhzemjv/files/e/0/2/dataset_e02e3022-5cb8-4a1a-837b-97a74809bd36.dat\n-galaxy.model.metadata DEBUG 2023-05-09 13:05:12,481 [pN:main.1,p:159691,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 2\n-\n-Shut down\n-supervisord has terminated\n-There were problems with 2 test(s) - out of 2 test(s) executed. See tool_test_output.html for detailed breakdown.\n-FROGS_preprocess (Test #1): failed\n-FROGS_preprocess (Test #2): failed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/test/taxo_affi.log --- a/test-data/test/taxo_affi.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1698 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp_1t0d9vn/galaxy-dev\n-Clonage dans \'/tmp/tmp_1t0d9vn/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.2 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b' environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-2048}/1024)) && taxonomic_affiliation.py --reference \'/home/vdarbot/Bureau/FROGS-wrappers/tools/frogs/test-data/databases/frogs_db_data/ITS1.rdp.fasta\' --taxonomy-ranks Domain Phylum Class Order Family Genus Species --input-biom \'/tmp/tmp_1t0d9vn/files/7/6/8/dataset_7684e6bd-7410-46ed-ac32-1bc9f98e4c8a.dat\' --input-fasta \'/tmp/tmp_1t0d9vn/files/4/f/1/dataset_4f106e37-c173-4a9f-ba80-a5a8566725ab.dat\' --output-biom \'/tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_129bd961-982f-4e88-b3d9-32169c06dfbb.dat\' --summary \'/tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_59c1907c-4060-4f2c-9634-d2b7f6659ecb.dat\' --nb-cpus ${GALAXY_SLOTS:-1} --java-mem $GALAXY_MEMORY_GB --rdp]\n-galaxy.jobs.runners DEBUG 2023-05-09 11:18:01,194 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] (3) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmp_1t0d9vn/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp_1t0d9vn/job_working_directory/000/3/galaxy_3.ec; \n-if [ -f "/tmp/tmp_1t0d9vn/job_working_directory/000/3/working/affiliation.biom" ] ; then cp "/tmp/tmp_1t0d9vn/job_working_directory/000/3/working/affiliation.biom" "/tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_129bd961-982f-4e88-b3d9-32169c06dfbb.dat" ; fi; \n-if [ -f "/tmp/tmp_1t0d9vn/job_working_directory/000/3/working/report.html" ] ; then cp "/tmp/tmp_1t0d9vn/job_working_directory/000/3/working/report.html" "/tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_59c1907c-4060-4f2c-9634-d2b7f6659ecb.dat" ; fi; cd \'/tmp/tmp_1t0d9vn/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-09 11:18:01,206 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] (3) executing job script: /tmp/tmp_1t0d9vn/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-09 11:18:05,850 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] check_pg(): No process found in process group 54104\n-galaxy.jobs.runners.local DEBUG 2023-05-09 11:18:05,850 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] execution finished: /tmp/tmp_1t0d9vn/job_working_directory/000/3/galaxy_3.sh\n-galaxy.jobs DEBUG 2023-05-09 11:18:05,899 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_129bd961-982f-4e88-b3d9-32169c06dfbb.dat to /tmp/tmp_1t0d9vn/files/1/2/9/dataset_129bd961-982f-4e88-b3d9-32169c06dfbb.dat\n-galaxy.jobs DEBUG 2023-05-09 11:18:05,899 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] finish(): Moved /tmp/tmp_1t0d9vn/job_working_directory/000/3/outputs/galaxy_dataset_59c1907c-4060-4f2c-9634-d2b7f6659ecb.dat to /tmp/tmp_1t0d9vn/files/5/9/c/dataset_59c1907c-4060-4f2c-9634-d2b7f6659ecb.dat\n-galaxy.model.metadata DEBUG 2023-05-09 11:18:05,930 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.model.metadata DEBUG 2023-05-09 11:18:05,939 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 4\n-galaxy.jobs DEBUG 2023-05-09 11:18:06,016 [pN:main.1,p:54014,tN:LocalRunner.work_thread-3] job_wrapper.finish for job 3 executed (123.811 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_taxonomic_affiliation (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/tool_test_output_all.html --- a/test-data/tool_test_output_all.html Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,291 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n- <head>\n- <meta charset="utf-8">\n- <meta http-equiv="X-UA-Compatible" content="IE=edge">\n- <meta name="viewport" content="width=device-width, initial-scale=1">\n- <title>Test Results (powered by Planemo)</title>\n-\n- <!-- Bootstrap -->\n- <style>/*!\n- * Bootstrap v3.3.1 (http://getbootstrap.com)\n- * Copyright 2011-2014 Twitter, Inc.\n- * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)\n- *//*! normalize.css v3.0.2 | MIT License | git.io/normalize */html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,menu,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background-color:transparent}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}dfn{font-style:italic}h1{margin:.67em 0;font-size:2em}mark{color:#000;background:#ff0}small{font-size:80%}sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:1em 40px}hr{height:0;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box}pre{overflow:auto}code,kbd,pre,samp{font-family:monospace,monospace;font-size:1em}button,input,optgroup,select,textarea{margin:0;font:inherit;color:inherit}button{overflow:visible}button,select{text-transform:none}button,html input[type=button],input[type=reset],input[type=submit]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0}input{line-height:normal}input[type=checkbox],input[type=radio]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;padding:0}input[type=number]::-webkit-inner-spin-button,input[type=number]::-webkit-outer-spin-button{height:auto}input[type=search]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield}input[type=search]::-webkit-search-cancel-button,input[type=search]::-webkit-search-decoration{-webkit-appearance:none}fieldset{padding:.35em .625em .75em;margin:0 2px;border:1px solid silver}legend{padding:0;border:0}textarea{overflow:auto}optgroup{font-weight:700}table{border-spacing:0;border-collapse:collapse}td,th{padding:0}/*! 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format(\'svg\')}.glyphicon{position:relative;top:1px;display:inline-block;font-family:\'Glyphi'..b"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'));\n- 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b |
diff -r b2967b704d6b -r f479218f3736 test-data/tree.log --- a/test-data/tree.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,6116 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmpeb913vpo/galaxy-dev\n-Clonage dans \'/tmp/tmpeb913vpo/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'a3/bin/activate\' \'/home/vdarbot/miniconda3/envs/mulled-v1-663b8adea9f89270af0e128d394b30e933a8f81efb8a32d25f7cdca23513d2c5\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; tree.py --input-sequences \'/tmp/tmptzzsg46p/files/f/6/7/dataset_f67e887f-af82-4a01-89bf-d98ea02d75f7.dat\' --biom-file \'/tmp/tmptzzsg46p/files/4/7/f/dataset_47fab374-6bc3-434c-8ace-d4be1ed43098.dat\' --nb-cpus ${GALAXY_SLOTS:-1} --out-tree \'/tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_d5f9f3dd-3929-4ff5-a24d-81dbe0035332.dat\' --html \'/tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_472c1815-c603-4fb0-9d4b-f0d2c9015184.dat\']\n-galaxy.jobs.runners DEBUG 2023-05-04 11:20:12,285 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] (3) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmptzzsg46p/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmptzzsg46p/job_working_directory/000/3/galaxy_3.ec; \n-if [ -f "/tmp/tmptzzsg46p/job_working_directory/000/3/working/tree.nwk" ] ; then cp "/tmp/tmptzzsg46p/job_working_directory/000/3/working/tree.nwk" "/tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_d5f9f3dd-3929-4ff5-a24d-81dbe0035332.dat" ; fi; \n-if [ -f "/tmp/tmptzzsg46p/job_working_directory/000/3/working/summary.html" ] ; then cp "/tmp/tmptzzsg46p/job_working_directory/000/3/working/summary.html" "/tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_472c1815-c603-4fb0-9d4b-f0d2c9015184.dat" ; fi; cd \'/tmp/tmptzzsg46p/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-05-04 11:20:12,299 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] (3) executing job script: /tmp/tmptzzsg46p/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-05-04 11:20:30,580 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] check_pg(): No process found in process group 181876\n-galaxy.jobs.runners.local DEBUG 2023-05-04 11:20:30,581 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] execution finished: /tmp/tmptzzsg46p/job_working_directory/000/3/galaxy_3.sh\n-galaxy.jobs DEBUG 2023-05-04 11:20:30,635 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_d5f9f3dd-3929-4ff5-a24d-81dbe0035332.dat to /tmp/tmptzzsg46p/files/d/5/f/dataset_d5f9f3dd-3929-4ff5-a24d-81dbe0035332.dat\n-galaxy.jobs DEBUG 2023-05-04 11:20:30,635 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] finish(): Moved /tmp/tmptzzsg46p/job_working_directory/000/3/outputs/galaxy_dataset_472c1815-c603-4fb0-9d4b-f0d2c9015184.dat to /tmp/tmptzzsg46p/files/4/7/2/dataset_472c1815-c603-4fb0-9d4b-f0d2c9015184.dat\n-galaxy.model.metadata DEBUG 2023-05-04 11:20:30,688 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.model.metadata DEBUG 2023-05-04 11:20:30,703 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 4\n-galaxy.jobs DEBUG 2023-05-04 11:20:30,794 [pN:main.1,p:181787,tN:LocalRunner.work_thread-0] job_wrapper.finish for job 3 executed (171.644 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_Tree (Test #1): passed\n' |
b |
diff -r b2967b704d6b -r f479218f3736 test-data/tsv_to_biom.log --- a/test-data/tsv_to_biom.log Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,1032 +0,0 @@\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.fetch \'+refs/*:refs/*\'\n-git --git-dir /home/vdarbot/.planemo/gx_repo config remote.origin.mirror true\n-git --git-dir /home/vdarbot/.planemo/gx_repo remote update >/dev/null 2>&1\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-git clone --branch master /home/vdarbot/.planemo/gx_repo /tmp/tmp983sks31/galaxy-dev\n-Clonage dans \'/tmp/tmp983sks31/galaxy-dev\'...\n-fait.\n-if [ -d .venv ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/vdarbot/.planemo/gx_venv_3; fi && export GALAXY_VIRTUAL_ENV && if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then /home/vdarbot/miniconda3/bin/virtualenv $GALAXY_VIRTUAL_ENV -p /home/vdarbot/miniconda3/bin/python3; echo "Created virtualenv"; fi && if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; echo "Activated a virtualenv for Galaxy"; echo "$VIRTUAL_ENV"; else echo "Failed to activate virtualenv."; fi && ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}\n-galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input\n-Activated a virtualenv for Galaxy\n-/home/vdarbot/.planemo/gx_venv_3\n-Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample\n-Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample\n-Initializing static/welcome.html from welcome.html.sample\n-Activating virtualenv at /home/vdarbot/.planemo/gx_venv_3\n-Requirement already satisfied: pip>=20.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (21.2.4)\n-Requirement already satisfied: wheel in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (0.37.0)\n-WARNING: You are using pip version 21.2.4; however, version 23.1.1 is available.\n-You should consider upgrading via the \'/home/vdarbot/.planemo/gx_venv_3/bin/python -m pip install --upgrade pip\' command.\n-Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple, https://wheels.galaxyproject.org/simple\n-Ignoring asynctest: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring cached-property: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring colorama: markers \'python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"\' don\'t match your environment\n-Ignoring numpy: markers \'python_version >= "3.7" and python_version < "3.8"\' don\'t match your environment\n-Ignoring pkgutil-resolve-name: markers \'python_version >= "3.7" and python_version < "3.9"\' don\'t match your environment\n-Ignoring pyreadline3: markers \'sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"\' don\'t match your environment\n-Ignoring pyreadline: markers \'sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"\' don\'t match your environment\n-Requirement already satisfied: a2wsgi==1.6.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.6.0)\n-Requirement already satisfied: adal==1.2.7 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.2.7)\n-Requirement already satisfied: aiofiles==22.1.0 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (22.1.0)\n-Requirement already satisfied: aiohttp==3.8.3 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.8.3)\n-Requirement already satisfied: aiosignal==1.3.1 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.3.1)\n-Requirement already satisfied: alembic-utils==0.7.8 in /home/vdarbot/.planemo/gx_venv_3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.7.8)\n-Requirement already satisfied: alembic==1.9.2 in /home/vda'..b'OUNT -lt $MAX_TRIES ]; do\n- . \'/home/vdarbot/miniconda3/bin/activate\' \'/home/vdarbot/miniconda3/envs/__frogs@4.1.0\' > conda_activate.log 2>&1\n- if [ $? -eq 0 ];then\n- break\n- else\n- let COUNT=COUNT+1\n- if [ $COUNT -eq $MAX_TRIES ];then\n- echo "Failed to activate conda environment! Error was:"\n- cat conda_activate.log\n- exit 1\n- fi\n- sleep 10s\n- fi\n-done\n-} ; tsv_to_biom.py --input-tsv \'/tmp/tmp983sks31/files/5/e/a/dataset_5eadd393-2680-4ca6-9e9b-e44a65ef8e5c.dat\' --output-biom \'/tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d869dda1-1a92-4598-a1f5-1474a87202f1.dat\' --input-multi-affi \'/tmp/tmp983sks31/files/0/e/d/dataset_0ed28cc9-6a1e-4fb0-83dd-dacc95e890b5.dat\' --output-fasta \'/tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d30d4afa-9491-47be-b5b7-42236b5ec488.dat\']\n-galaxy.jobs.runners DEBUG 2023-04-26 10:47:14,358 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] (3) command is: mkdir -p working outputs configs\n-if [ -d _working ]; then\n- rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs\n-else\n- cp -R working _working; cp -R outputs _outputs; cp -R configs _configs\n-fi\n-cd working; /bin/bash /tmp/tmp983sks31/job_working_directory/000/3/tool_script.sh > \'../outputs/tool_stdout\' 2> \'../outputs/tool_stderr\'; return_code=$?; echo $return_code > /tmp/tmp983sks31/job_working_directory/000/3/galaxy_3.ec; \n-if [ -f "/tmp/tmp983sks31/job_working_directory/000/3/working/abundance.biom" ] ; then cp "/tmp/tmp983sks31/job_working_directory/000/3/working/abundance.biom" "/tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d869dda1-1a92-4598-a1f5-1474a87202f1.dat" ; fi; \n-if [ -f "/tmp/tmp983sks31/job_working_directory/000/3/working/seed.fasta" ] ; then cp "/tmp/tmp983sks31/job_working_directory/000/3/working/seed.fasta" "/tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d30d4afa-9491-47be-b5b7-42236b5ec488.dat" ; fi; cd \'/tmp/tmp983sks31/job_working_directory/000/3\'; \n-[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True; python metadata/set.py; sh -c "exit $return_code"\n-galaxy.jobs.runners.local DEBUG 2023-04-26 10:47:14,408 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] (3) executing job script: /tmp/tmp983sks31/job_working_directory/000/3/galaxy_3.sh\n-\n-galaxy.jobs.runners.util.process_groups DEBUG 2023-04-26 10:47:20,391 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] check_pg(): No process found in process group 209044\n-galaxy.jobs.runners.local DEBUG 2023-04-26 10:47:20,392 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] execution finished: /tmp/tmp983sks31/job_working_directory/000/3/galaxy_3.sh\n-galaxy.jobs DEBUG 2023-04-26 10:47:20,427 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d869dda1-1a92-4598-a1f5-1474a87202f1.dat to /tmp/tmp983sks31/files/d/8/6/dataset_d869dda1-1a92-4598-a1f5-1474a87202f1.dat\n-galaxy.jobs DEBUG 2023-04-26 10:47:20,427 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] finish(): Moved /tmp/tmp983sks31/job_working_directory/000/3/outputs/galaxy_dataset_d30d4afa-9491-47be-b5b7-42236b5ec488.dat to /tmp/tmp983sks31/files/d/3/0/dataset_d30d4afa-9491-47be-b5b7-42236b5ec488.dat\n-galaxy.model.metadata DEBUG 2023-04-26 10:47:20,457 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3\n-galaxy.model.metadata DEBUG 2023-04-26 10:47:20,466 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 4\n-galaxy.jobs DEBUG 2023-04-26 10:47:20,552 [pN:main.1,p:208934,tN:LocalRunner.work_thread-1] job_wrapper.finish for job 3 executed (132.107 ms)\n-\n-Shut down\n-supervisord has terminated\n-All 1 test(s) executed passed.\n-FROGS_tsv_to_biom (Test #1): passed\n' |
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diff -r b2967b704d6b -r f479218f3736 tool-data/frogs_picrust2_default_dir.loc.sample --- a/tool-data/frogs_picrust2_default_dir.loc.sample Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,42 +0,0 @@ -# Copyright (C) 2022 INRA -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. -# -# -#This is a sample file that enables tools FROGS_frogsfunc_placeseqs to place -#studies sequences (i.e. OTUs) into a reference tree. -# -#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult -#PICRUSt2 documentation to find out where they are located in your environment. -# -#If you are not comfortable with picrust2 command lines, just create .loc files -#with EXAMPLE FOR TEST files remembering to replace <Galaxy_dir> with the real path. -# -#The indicated path is the one if you do not change the default galaxy config of conda directory. -# -#<identifiant> <marker_gene> <path_to_default_dir> <path_to_marker_copy_numbers> <placement_tool> -# -#default dir must contain these files: -# -#-rw-rw-r-- 1 vdarbot vdarbot 31922081 avril 1 2021 pro_ref.fna -#-rwxrwxr-x 1 vdarbot vdarbot 272826 avril 1 2021 pro_ref.hmm -#-rwxrwxr-x 1 vdarbot vdarbot 116 avril 1 2021 pro_ref.model -#-rwxrwxr-x 1 vdarbot vdarbot 1707 avril 1 2021 pro_ref.raxml_info -#-rwxrwxr-x 1 vdarbot vdarbot 600048 avril 1 2021 pro_ref.tre -# -# EXAMPLE FOR TEST : -#picrust2_default_dir_16S 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryiotic/pro_ref/16S_counts.txt.gz epa-ng -#picrust2_default_dir_16S 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryiotic/pro_ref/16S_counts.txt.gz sepp -#picrust2_default_dir_ITS ITS <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_ITS/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryiotic/fungi/fungi_ITS/ITS_counts.txt.gz epa-ng -#picrust2_default_dir_18S 18S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_18S/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryiotic/fungi/fungi_18S/18S_counts.txt.gz epa-ng |
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diff -r b2967b704d6b -r f479218f3736 tool-data/frogs_picrust2_functions.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/frogs_picrust2_functions.loc.sample Tue Jun 13 06:59:09 2023 +0000 |
b |
@@ -0,0 +1,45 @@ +# Copyright (C) 2022 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_frogsfunc_copynumbers to predict +#the copy number of gene families present in the predicted genome for OTU, +# given a tree and a set of known trait values (FROGS_frogsfunc_placeseqs). +# +#PICRUSt2 files are present in the arborescence of PICRUSt2. +# +#<marker_gene> <db> <picrust2_input_marker> <picrust2_input_function> +# +# For 16S data (see the 6 first lines), PICRUSt2 only takes the dname of the database as input (for exemple EC). +# With ITS and 18S data, you have to specify the path of marker gene counts files. +# +# +# Bellow you will find out how to implement this loc file. +# +# The indicated path is the one if you do not change the default galaxy config of conda directory. +# Just adapt path by replacing <Galaxy_dir> with the real path and eventually the picrust version. +# +# If you are not using this default conda behavior, please consult PICRUSt2 documentation to find out where they are located in your environment. +# +# +# +#16S EC EC EC 2.5.1 +#16S KO KO KO 2.5.1 +#16S PFAM PFAM PFAM 2.5.1 +#16S COG COG COG 2.5.1 +#16S TIGRFAM TIGRFAM TIGRFAM 2.5.1 +#16S PHENO PHENO PHENO 2.5.1 +#ITS EC <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ITS_counts.txt.gz <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ec_ITS_counts.txt.gz 2.5.1 +#18S EC <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/18S_counts.txt.gz <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ec_18S_counts.txt.gz 2.5.1 |
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diff -r b2967b704d6b -r f479218f3736 tool-data/frogs_picrust2_marker_table.loc.sample --- a/tool-data/frogs_picrust2_marker_table.loc.sample Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,45 +0,0 @@ -# Copyright (C) 2022 INRA -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. -# -# -#This is a sample file that enables tools FROGS_frogsfunc_copynumbers to predict -#the copy number of gene families present in the predicted genome for OTU, -# given a tree and a set of known trait values (FROGS_frogsfunc_placeseqs). -# -#PICRUSt2 files are present in the arborescence of PICRUSt2. -# -#<marker_gene> <db> <picrust2_input_marker> <picrust2_input_function> -# -# For 16S data (see the 6 first lines), PICRUSt2 only takes the dname of the database as input (for exemple EC). -# With ITS and 18S data, you have to specify the path of marker gene counts files. -# -# -# Bellow you will find out how to implement this loc file. -# -# The indicated path is the one if you do not change the default galaxy config of conda directory. -# Just adapt path by replacing <Galaxy_dir> with the real path and eventually the picrust version. -# -# If you are not using this default conda behavior, please consult PICRUSt2 documentation to find out where they are located in your environment. -# -# -# -#16S EC EC EC -#16S KO KO KO -#16S PFAM PFAM PFAM -#16S COG COG COG -#16S TIGRFAM TIGRFAM TIGRFAM -#16S PHENO PHENO PHENO -#ITS EC <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ITS_counts.txt.gz <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ec_ITS_counts.txt.gz -#18S EC <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/18S_counts.txt.gz <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ec_18S_counts.txt.gz |
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diff -r b2967b704d6b -r f479218f3736 tool-data/frogs_picrust2_pathway_map.loc.sample --- a/tool-data/frogs_picrust2_pathway_map.loc.sample Tue May 23 07:59:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
b |
@@ -1,37 +0,0 @@ -# Copyright (C) 2022 INRA -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. -# -# -#This is a sample file that enables tools FROGS_frogsfunc_pathways to map pathways to reactions. -#The default mapfile maps MetaCyc reactions to prokaryotic MetaCyc pathways. -# -#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult -#PICRUSt2 documentation to find out where they are located in your environment. -# -#If you are not comfortable with picrust2 command lines, just create .loc files -#with EXAMPLE FOR TEST files remembering to replace <Galaxy_dir> with the real path. -# -#The indicated path is the one if you do not change the default galaxy config of conda directory. -# -#<db_id> <db_name> <marker_gene> <path_to_mapfiles> -# -# -# -# -# EXAMPLE FOR TEST : -#pro_metacyc_pathway Metacyc 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt -#fungi_metacyc_pathway Metacyc ITS <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi.txt -#fungi_metacyc_pathway Metacyc 18S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi.txt -#kegg_modules_pathway Kegg 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv \ No newline at end of file |
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diff -r b2967b704d6b -r f479218f3736 tool-data/frogs_picrust2_pathways.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/frogs_picrust2_pathways.loc.sample Tue Jun 13 06:59:09 2023 +0000 |
b |
@@ -0,0 +1,37 @@ +# Copyright (C) 2022 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_frogsfunc_pathways to map pathways to reactions. +#The default mapfile maps MetaCyc reactions to prokaryotic MetaCyc pathways. +# +#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult +#PICRUSt2 documentation to find out where they are located in your environment. +# +#If you are not comfortable with picrust2 command lines, just create .loc files +#with EXAMPLE FOR TEST files remembering to replace <Galaxy_dir> with the real path. +# +#The indicated path is the one if you do not change the default galaxy config of conda directory. +# +#<db_id> <db_name> <marker_gene> <path_to_mapfiles> <picrust_version> +# +# +# +# +# EXAMPLE FOR TEST : +#pro_metacyc_pathway Metacyc 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt 2.5.1 +#fungi_metacyc_pathway Metacyc ITS <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi.txt 2.5.1 +#fungi_metacyc_pathway Metacyc 18S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi.txt 2.5.1 +#kegg_modules_pathway Kegg 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv 2.5.1 \ No newline at end of file |
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diff -r b2967b704d6b -r f479218f3736 tool-data/frogs_picrust2_placeseqs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/frogs_picrust2_placeseqs.loc.sample Tue Jun 13 06:59:09 2023 +0000 |
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@@ -0,0 +1,42 @@ +# Copyright (C) 2022 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +# +#This is a sample file that enables tools FROGS_frogsfunc_placeseqs to place +#studies sequences (i.e. OTUs) into a reference tree. +# +#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult +#PICRUSt2 documentation to find out where they are located in your environment. +# +#If you are not comfortable with picrust2 command lines, just create .loc files +#with EXAMPLE FOR TEST files remembering to replace <Galaxy_dir> with the real path. +# +#The indicated path is the one if you do not change the default galaxy config of conda directory. +# +#<identifiant> <marker_gene> <path_to_default_dir> <path_to_marker_copy_numbers> <placement_tool> <picrust_version> +# +#default dir must contain these files: +# +#-rw-rw-r-- 1 vdarbot vdarbot 31922081 avril 1 2021 pro_ref.fna +#-rwxrwxr-x 1 vdarbot vdarbot 272826 avril 1 2021 pro_ref.hmm +#-rwxrwxr-x 1 vdarbot vdarbot 116 avril 1 2021 pro_ref.model +#-rwxrwxr-x 1 vdarbot vdarbot 1707 avril 1 2021 pro_ref.raxml_info +#-rwxrwxr-x 1 vdarbot vdarbot 600048 avril 1 2021 pro_ref.tre +# +# EXAMPLE FOR TEST : +#picrust2_default_dir_16S 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/16S_counts.txt.gz epa-ng 2.5.1 +#picrust2_default_dir_16S 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/16S_counts.txt.gz sepp 2.5.1 +#picrust2_default_dir_ITS ITS <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_ITS/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ITS_counts.txt.gz epa-ng 2.5.1 +#picrust2_default_dir_18S 18S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_18S/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/18S_counts.txt.gz epa-ng 2.5.1 |
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diff -r b2967b704d6b -r f479218f3736 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue May 23 07:59:04 2023 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 13 06:59:09 2023 +0000 |
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@@ -13,24 +13,19 @@ <file path="${__HERE__}/tool-data/frogs_contaminant_db.loc" /> </table> <!-- Locations of picrust2 default directory --> - <table name="frogs_picrust2_default_dir" comment_char="#"> - <columns>value, name, dir, path, placement_tool</columns> - <file path="${__HERE__}/tool-data/frogs_picrust2_default_dir.loc" /> - </table> - <!-- Locations of picrust2 description files directory --> - <table name="frogs_picrust2_description_dir" comment_char="#"> - <columns>value, name, path</columns> - <file path="${__HERE__}/tool-data/frogs_picrust2_description_dir.loc" /> + <table name="frogs_picrust2_placeseqs" comment_char="#"> + <columns>value, name, dir, path, placement_tool, version</columns> + <file path="${__HERE__}/tool-data/frogs_picrust2_placeseqs.loc" /> </table> <!-- Locations of picrust2 marker table files --> - <table name="frogs_picrust2_marker_table" comment_char="#"> - <columns>value, name, path, traits</columns> - <file path="${__HERE__}/tool-data/frogs_picrust2_marker_table.loc" /> + <table name="frogs_picrust2_functions" comment_char="#"> + <columns>value, name, path, traits, version</columns> + <file path="${__HERE__}/tool-data/frogs_picrust2_functions.loc" /> </table> <!-- Locations of picrust2 traits table files --> <!-- Locations of picrust2 pathway map files --> - <table name="frogs_picrust2_pathway_map" comment_char="#"> - <columns>marker, path, value, name </columns> - <file path="${__HERE__}/tool-data/frogs_picrust2_pathway_map.loc" /> + <table name="frogs_picrust2_pathways" comment_char="#"> + <columns>marker, path, value, name, version </columns> + <file path="${__HERE__}/tool-data/frogs_picrust2_pathways.loc" /> </table> </tables> \ No newline at end of file |
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diff -r b2967b704d6b -r f479218f3736 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Tue May 23 07:59:04 2023 +0000 +++ b/tool_data_table_conf.xml.test Tue Jun 13 06:59:09 2023 +0000 |
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@@ -13,18 +13,18 @@ <file path="${__HERE__}/test-data/databases/frogs_contaminant_db.loc" /> </table> <!-- Locations of picrust2 default directory --> - <table name="frogs_picrust2_default_dir" comment_char="#"> + <table name="frogs_picrust2_placeseqs" comment_char="#"> <columns>value, name, dir, path, placement_tool</columns> - <file path="${__HERE__}/test-data/databases/frogs_picrust2_default_dir.loc" /> + <file path="${__HERE__}/test-data/databases/frogs_picrust2_placeseqs.loc" /> </table> <!-- Locations of picrust2 marker table files --> - <table name="frogs_picrust2_marker_table" comment_char="#"> + <table name="frogs_picrust2_functions" comment_char="#"> <columns>value, name, path, traits</columns> - <file path="${__HERE__}/test-data/databases/frogs_picrust2_marker_table.loc" /> + <file path="${__HERE__}/test-data/databases/frogs_picrust2_functions.loc" /> </table> <!-- Locations of picrust2 pathway map files --> - <table name="frogs_picrust2_pathway_map" comment_char="#"> + <table name="frogs_picrust2_pathways" comment_char="#"> <columns>marker, path, value, name </columns> - <file path="${__HERE__}/test-data/databases/frogs_picrust2_pathway_map.loc" /> + <file path="${__HERE__}/test-data/databases/frogs_picrust2_pathways.loc" /> </table> </tables> \ No newline at end of file |