| Previous changeset 0:1563554bb3f0 (2016-08-01) Next changeset 2:34635f944495 (2016-11-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd |
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modified:
run_de_analysis.xml tool_dependencies.xml |
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added:
test-data/count/express_bowtie/sample_A test-data/count/express_bowtie/sample_B test-data/count/rsem_bowtie/sample_A test-data/count/rsem_bowtie/sample_B test-data/count/rsem_bowtie2/sample_A test-data/count/rsem_bowtie2/sample_B test-data/count/salmon/sample_A test-data/count/salmon/sample_B test-data/samples.tsv |
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removed:
test-data/count/express_bowtie/results.xprs.genes test-data/count/express_bowtie/results_B.xprs.genes test-data/count/rsem_bowtie/RSEM.genes.results test-data/count/rsem_bowtie/RSEM.genes_B.results test-data/count/rsem_bowtie2/RSEM.genes.results test-data/count/rsem_bowtie2/RSEM.genes_B.results test-data/count/salmon/quant.sf test-data/count/salmon/quant.sf.genes |
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| diff -r 1563554bb3f0 -r 18213f29e0b9 run_de_analysis.xml --- a/run_de_analysis.xml Mon Aug 01 14:43:38 2016 -0400 +++ b/run_de_analysis.xml Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.0"> +<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.1"> <description>using a Trinity assembly</description> <macros> <import>macros.xml</import> @@ -159,6 +159,8 @@ ConditionC CondC_replicate3 =========== ================ + +This file can be generated with the 'Describe samples and replicates' tool. It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'. The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'. |
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| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/express_bowtie/results.xprs.genes --- a/test-data/count/express_bowtie/results.xprs.genes Mon Aug 01 14:43:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm -NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN2_c2_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 -NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN0_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN1_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 -NA TRINITY_DN2_c1_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/express_bowtie/results_B.xprs.genes --- a/test-data/count/express_bowtie/results_B.xprs.genes Mon Aug 01 14:43:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm -NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN2_c1_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 -NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN0_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 -NA TRINITY_DN1_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN2_c2_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/express_bowtie/sample_A --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/sample_A Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c2_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 +NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN0_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN1_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 +NA TRINITY_DN2_c1_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/express_bowtie/sample_B --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/sample_B Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c1_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 +NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN0_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 +NA TRINITY_DN1_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c2_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/rsem_bowtie/RSEM.genes.results --- a/test-data/count/rsem_bowtie/RSEM.genes.results Mon Aug 01 14:43:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 -TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 -TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 -TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 -TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 -TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 -TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/rsem_bowtie/RSEM.genes_B.results --- a/test-data/count/rsem_bowtie/RSEM.genes_B.results Mon Aug 01 14:43:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 -TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 -TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 -TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 -TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 -TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 -TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/rsem_bowtie/sample_A --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/sample_A Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/rsem_bowtie/sample_B --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/sample_B Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/rsem_bowtie2/RSEM.genes.results --- a/test-data/count/rsem_bowtie2/RSEM.genes.results Mon Aug 01 14:43:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 -TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 -TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 -TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 -TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 -TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 -TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/rsem_bowtie2/RSEM.genes_B.results --- a/test-data/count/rsem_bowtie2/RSEM.genes_B.results Mon Aug 01 14:43:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 -TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 -TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 -TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 -TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 -TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 -TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/rsem_bowtie2/sample_A --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/sample_A Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/rsem_bowtie2/sample_B --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/sample_B Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/salmon/quant.sf --- a/test-data/count/salmon/quant.sf Mon Aug 01 14:43:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -Name Length EffectiveLength TPM NumReads -TRINITY_DN1_c0_g1_i1 380 120.403 179183 13 -TRINITY_DN0_c0_g1_i1 229 229 55271.5 7.62686 -TRINITY_DN2_c0_g1_i1 279 31.1522 565494 10.6151 -TRINITY_DN2_c1_g1_i1 541 278.129 113370 19 -TRINITY_DN2_c2_g1_i1 240 240 32900.7 4.75801 -TRINITY_DN2_c3_g1_i1 202 202 0 0 -TRINITY_DN3_c0_g1_i1 216 216 53781.8 7 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/salmon/quant.sf.genes --- a/test-data/count/salmon/quant.sf.genes Mon Aug 01 14:43:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -Name Length EffectiveLength TPM NumReads -TRINITY_DN2_c2_g1 240.00 240.00 32900.70 4.76 -TRINITY_DN0_c0_g1 229.00 229.00 55271.50 7.63 -TRINITY_DN1_c0_g1 380.00 120.40 179183.00 13.00 -TRINITY_DN2_c0_g1 279.00 31.15 565494.00 10.62 -TRINITY_DN2_c3_g1 202.00 202.00 0.00 0.00 -TRINITY_DN3_c0_g1 216.00 216.00 53781.80 7.00 -TRINITY_DN2_c1_g1 541.00 278.13 113370.00 19.00 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/salmon/sample_A --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/salmon/sample_A Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +Name Length EffectiveLength TPM NumReads +TRINITY_DN1_c0_g1_i1 380 120.403 179183 13 +TRINITY_DN0_c0_g1_i1 229 229 55271.5 7.62686 +TRINITY_DN2_c0_g1_i1 279 31.1522 565494 10.6151 +TRINITY_DN2_c1_g1_i1 541 278.129 113370 19 +TRINITY_DN2_c2_g1_i1 240 240 32900.7 4.75801 +TRINITY_DN2_c3_g1_i1 202 202 0 0 +TRINITY_DN3_c0_g1_i1 216 216 53781.8 7 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/count/salmon/sample_B --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/salmon/sample_B Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +Name Length EffectiveLength TPM NumReads +TRINITY_DN2_c2_g1 240.00 240.00 32900.70 4.76 +TRINITY_DN0_c0_g1 229.00 229.00 55271.50 7.63 +TRINITY_DN1_c0_g1 380.00 120.40 179183.00 13.00 +TRINITY_DN2_c0_g1 279.00 31.15 565494.00 10.62 +TRINITY_DN2_c3_g1 202.00 202.00 0.00 0.00 +TRINITY_DN3_c0_g1 216.00 216.00 53781.80 7.00 +TRINITY_DN2_c1_g1 541.00 278.13 113370.00 19.00 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 test-data/samples.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples.tsv Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -0,0 +1,4 @@ +ConditionA CondA_replicate1 +ConditionA CondA_replicate2 +ConditionB CondB_replicate1 +ConditionB CondB_replicate2 |
| b |
| diff -r 1563554bb3f0 -r 18213f29e0b9 tool_dependencies.xml --- a/tool_dependencies.xml Mon Aug 01 14:43:38 2016 -0400 +++ b/tool_dependencies.xml Fri Nov 18 06:08:32 2016 -0500 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="trinity" version="2.2.0"> - <repository changeset_revision="729219ec7049" name="package_trinity_2_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="76d63b5c571a" name="package_trinity_2_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="bowtie" version="1.1.2"> <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> @@ -9,11 +9,8 @@ <package name="bowtie2" version="2.2.6"> <repository changeset_revision="0d9cd7487cc9" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="samtools" version="1.2"> - <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> <package name="bioconductor-edger" version="3.14.0"> - <repository changeset_revision="8ed6cfd2b21f" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="5f4abad5b2c1" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="rsem" version="1.2.28"> <repository changeset_revision="4567331d510a" name="package_rsem_1_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> @@ -22,7 +19,7 @@ <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="bioconductor-limma" version="3.28.10"> - <repository changeset_revision="fc78b4bbe0ab" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b313488c66bd" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="deseq2" version="1.10.0"> <repository changeset_revision="e4a11a7d33d6" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> |