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diff unified_genotyper.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 7533db8dfb5b
children fd9d089a9ff4
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line diff
--- a/unified_genotyper.xml	Mon Feb 18 11:17:32 2013 -0600
+++ b/unified_genotyper.xml	Mon Feb 18 15:48:46 2013 -0600
@@ -20,7 +20,8 @@
     --out "${output_vcf}"
     --metrics_file "${output_metrics}"
     \$GATK2_SITE_OPTIONS
-    \$GATK2_THREAD_OPTIONS
+    \$GATK2_NUM_THREADS
+    \$GATK2_NUM_CPU_THREADS
     ##-et "NO_ET" -K "\$GATK2_BASE/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":