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diff base_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 6460f2ba6a60
children b99c25b0ad4d
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line diff
--- a/base_recalibrator.xml	Mon Feb 18 11:17:32 2013 -0600
+++ b/base_recalibrator.xml	Mon Feb 18 15:48:46 2013 -0600
@@ -15,7 +15,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "BaseRecalibrator"
     \$GATK2_SITE_OPTIONS
-    ## \$GATK2_THREAD_OPTIONS
+    \$GATK2_CPU_THREADS
     ##--num_threads 4 ##hard coded, for now
     ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout