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diff variant_recalibrator.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 a5c55503d196
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--- a/variant_recalibrator.xml	Mon Feb 18 11:17:32 2013 -0600
+++ b/variant_recalibrator.xml	Mon Feb 18 15:48:46 2013 -0600
@@ -13,7 +13,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "VariantRecalibrator"
     \$GATK2_SITE_OPTIONS
-    \$GATK2_THREAD_OPTIONS
+    \$GATK2_NUM_THREADS
     ##--num_threads 4 ##hard coded, for now
     ##-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