# HG changeset patch
# User jjohnson
# Date 1513090902 18000
# Node ID 3a4876d01c7e14147a53c4a4a17b4cce5d2bfffc
# Parent  4fe2e80d4ae13ad4a69b7963fd6c38d6f3125850
Uploaded

diff -r 4fe2e80d4ae1 -r 3a4876d01c7e ._defuse.xml
Binary file ._defuse.xml has changed
diff -r 4fe2e80d4ae1 -r 3a4876d01c7e datamanager_create_reference.xml
--- 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)"
diff -r 4fe2e80d4ae1 -r 3a4876d01c7e defuse.xml
--- 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>
 
diff -r 4fe2e80d4ae1 -r 3a4876d01c7e tool_dependencies.xml
--- 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>