# HG changeset patch
# User jjohnson
# Date 1361216019 18000
# Node ID 10c2fe2d3b3979632688f68a87820262efbca1ec

Uploaded

diff -r 000000000000 -r 10c2fe2d3b39 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Feb 18 14:33:39 2013 -0500
@@ -0,0 +1,48 @@
+<?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-2.3-9-gdcdccbb.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_NUM_THREADS" action="set_to">"--num_threads 4"</environment_variable>
+                    <environment_variable name="GATK2_NUM_CPU_THREADS" action="set_to">"--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>
+    </package>
+</tool_dependency>