Mercurial > repos > jjohnson > gatk2

diff tool_dependencies.xml @ 18:7533db8dfb5b draft

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Update tool_dependencies to GATK v 2.3
author Jim Johnson <jj@umn.edu>
date Thu, 20 Dec 2012 11:01:55 -0600
parents 35c6289faeff
children 09e6427d3e6a
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/tool_dependencies.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="gatk" version="2.2">
+    <package name="gatk" version="2.3">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2</action>
+                <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-2.3-4-gb8f1308.tar.bz2</action>
                 <action type="move_file">
                     <source>GenomeAnalysisTKLite.jar</source>
                     <destination>$INSTALL_DIR</destination>
@@ -15,7 +15,8 @@
                 </action>
                 <action type="set_environment">
                     <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">"--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD"</environment_variable>
+                    <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">"--phone_home STANDARD"</environment_variable>
+                    <environment_variable name="GATK2_THREAD_OPTIONS" action="set_to">"--num_threads 4 --num_cpu_threads_per_data_thread 3"</environment_variable>
                 </action>
             </actions>
         </install>