Mercurial > repos > jjohnson > defuse
changeset 13:3a4876d01c7e draft
Uploaded
| author | jjohnson |
|---|---|
| date | Tue, 12 Dec 2017 10:01:42 -0500 |
| parents | 4fe2e80d4ae1 |
| children | 038a5210392a |
| files | ._defuse.xml datamanager_create_reference.xml defuse.xml tool_dependencies.xml |
| diffstat | 4 files changed, 13 insertions(+), 11 deletions(-) [+] |
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--- a/datamanager_create_reference.xml Tue May 03 15:18:11 2016 -0400 +++ b/datamanager_create_reference.xml Tue Dec 12 10:01:42 2017 -0500 @@ -1,12 +1,12 @@ <tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="1.6.1" tool_type="manage_data"> <description>create a defuse reference from Ensembl and UCSC sources</description> - <requirements> - <requirement type="package" version="0.6.1">defuse</requirement> - <requirement type="package" version="0.1.18">samtools</requirement> - <requirement type="package" version="1.0.0">bowtie</requirement> - <requirement type="package" version="2013-05-09">gmap</requirement> - <requirement type="package" version="latest">kent</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <expand macro="defuse_requirement" /> + <expand macro="mapping_requirements" /> + </requirements> <command interpreter="python"> datamanager_create_reference.py --dbkey $genome.ensembl_genome_version --description "$genome.ensembl_prefix $genome.ensembl_genome_version ($genome.ucsc_genome_version)"
--- a/defuse.xml Tue May 03 15:18:11 2016 -0400 +++ b/defuse.xml Tue Dec 12 10:01:42 2017 -0500 @@ -626,7 +626,8 @@ mkdir -p output_dir #end if ## run defuse.pl -perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS +perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS; +exit_code_for_galaxy=\$?; ## copy primary results to output datasets if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi @@ -666,6 +667,7 @@ results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.dataset.extra_files_path fi #end if +(exit \$exit_code_for_galaxy) </configfile> </configfiles>
--- a/tool_dependencies.xml Tue May 03 15:18:11 2016 -0400 +++ b/tool_dependencies.xml Tue Dec 12 10:01:42 2017 -0500 @@ -1,10 +1,10 @@ <?xml version="1.0"?> <tool_dependency> <package name="defuse" version="0.6.2"> - <repository changeset_revision="5a4237bbe6bf" name="package_defuse_0_6_2" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="86278e018303" name="package_defuse_0_6_2" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.19"> - <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="bowtie" version="1.0.0"> <repository changeset_revision="9fcaaedbbfd6" name="package_bowtie_1_0_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> @@ -19,6 +19,6 @@ <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="ada" version="2.0.3"> - <repository changeset_revision="f0e6af8a95e5" name="package_r_ada_2_0_3" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="73f89898eb2a" name="package_r_ada_2_0_3" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>