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diff indel_realigner.xml @ 28:6ef8eb568700 draft

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Move GATK tool_dependency to a repository dependency, use 2 env vars: GATK2_NUM_THREADS and GATK2_NUM_CPU_THREADS for site threading values
author Jim Johnson <jj@umn.edu>
date Mon, 18 Feb 2013 15:48:46 -0600
parents 3924f62cd4e7
children 76f8ca47b810
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--- a/indel_realigner.xml	Mon Feb 18 11:17:32 2013 -0600
+++ b/indel_realigner.xml	Mon Feb 18 15:48:46 2013 -0600
@@ -16,7 +16,7 @@
     -T "IndelRealigner"
     -o "${output_bam}"
     \$GATK2_SITE_OPTIONS
-    ## \$GATK2_THREAD_OPTIONS
+    ## \$GATK2_NUM_THREADS 
     ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
     ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout