diff tool_dependencies.xml @ 28:6ef8eb568700 draft

Move GATK tool_dependency to a repository dependency, use 2 env vars: GATK2_NUM_THREADS and GATK2_NUM_CPU_THREADS for site threading values

--- a/tool_dependencies.xml	Mon Feb 18 11:17:32 2013 -0600
+++ b/tool_dependencies.xml	Mon Feb 18 15:48:46 2013 -0600
@@ -1,48 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="gatk" version="2.3">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-2.3-4-gb8f1308.tar.bz2</action>
-                <action type="move_file">
-                    <source>GenomeAnalysisTKLite.jar</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action>
-                <action type="move_file">
-                    <source>GenomeAnalysisTK.jar</source>
-                    <destination>$INSTALL_DIR</destination>
-                </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">"--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>
-        <readme>
-The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed:
-
- haplotypecaller                 
-   HaplotypeCaller               Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an 
-                                 active region.
-   HaplotypeResolver             Haplotype-based resolution of variants in 2 different eval files.
-
- reducereads                     
-   CompareBAM                    Given two BAMs with different read groups, it compares them based on ReduceReads 
-                                 metrics.
-   ReduceReads                   Reduces the BAM file using read based compression that keeps only essential information 
-                                 for variant calling
-                                 
-
-See: http://www.appistry.com/gatk/gatk-faqs-static for Licensing details.
-The full GATK build can be acquired from:  http://www.broadinstitute.org/gatk/download 
-and GenomeAnalysisTK.jar need to be manually installed into the GATK2_PATH set for the GenomeAnalysisTKLite.jar
-
-The GATK2_SITE_OPTIONS environment variable can be modified in the env.sh in the tool_dependencies path can be modified 
-for the local installation.  
-
-        </readme>
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="gatk_lite_2_3_9" owner="jjohnson" changeset_revision="10c2fe2d3b39" />
     </package>
     <package name="samtools" version="0.1.18">
         <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_samtools_0_1_18" owner="devteam" changeset_revision="5f7ec5048224" />