# HG changeset patch
# User david-hoover
# Date 1347467931 14400
# Node ID b138c556923173dac86ec128591f8fffc84df202
# Parent  07d3765a50ad983cd277fd9500350545178d2f9a
Uploaded

diff -r 07d3765a50ad -r b138c5569231 README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Wed Sep 12 12:38:51 2012 -0400
@@ -0,0 +1,9 @@
+The gatk2_sorted_picard_index.loc and gatk2_annotations.txt files must be
+copied into the tool-data directory.  The file tool_data_table_conf.xml must
+be edited to include references to these two new files.  
+
+Additionally, copies of or links to the GenomeAnalysisTK.jar and key file
+must be made within the directory tool-data/shared/jars/gatk2.
+
+  ${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk2/GenomeAnalysisTK.jar
+  ${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk2/gatk2_key_file
diff -r 07d3765a50ad -r b138c5569231 unified_genotyper.xml
--- a/unified_genotyper.xml	Wed Sep 12 12:13:25 2012 -0400
+++ b/unified_genotyper.xml	Wed Sep 12 12:38:51 2012 -0400
@@ -14,12 +14,12 @@
        #end if
    #end for
    -p 'java 
-    -jar "GenomeAnalysisTK.jar"
+    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk2/GenomeAnalysisTK.jar"
     -T "UnifiedGenotyper"
     --num_threads 4 ##hard coded, for now
     --out "${output_vcf}"
     --metrics_file "${output_metrics}"
-    -et "NO_ET" -K "gatk2_key_file" ##ET no phone home
+    -et "NO_ET" -K "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk2/gatk2_key_file" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"