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changeset 1:9b8e2a158073 draft

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Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
author Jim Johnson <jj@umn.edu>
date Thu, 01 Nov 2012 13:44:41 -0500
parents 74c05070a3f8
children a65944bad5c1
files tool_dependencies.xml unified_genotyper.xml
diffstat 2 files changed, 6 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Nov 01 13:53:22 2012 -0400
+++ b/tool_dependencies.xml	Thu Nov 01 13:44:41 2012 -0500
@@ -4,8 +4,12 @@
         <install version="1.0">
             <actions>
                 <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-latest.tar.bz2</action>
+                <!-- this expands into GenomeAnalysisTKLite-2.2-2-gd3f5a5e/
+                     which common_util.py tar_extraction_directory() does not find
+                     so the move file must contain the GenomeAnalysisTKLite-2.2-2-gd3f5a5e dir path
+                 -->
                 <action type="move_file">
-                    <source>GenomeAnalysisTKLite.jar</source>
+                    <source>GenomeAnalysisTKLite-2.2-2-gd3f5a5e/GenomeAnalysisTKLite.jar</source>
                     <destination>$INSTALL_DIR/GenomeAnalysisTK.jar</destination>
                 </action>
                 <action type="set_environment">
--- a/unified_genotyper.xml	Thu Nov 01 13:53:22 2012 -0400
+++ b/unified_genotyper.xml	Thu Nov 01 13:44:41 2012 -0500
@@ -2,7 +2,7 @@
   <description>SNP and indel caller</description>
   <requirements>
       <requirement type="package" version="2.2">gatk</requirement>
-      <requirement type="package" version="0.1.18" version="0.1.18">samtools</requirement>
+      <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
    --max_jvm_heap_fraction "1"