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diff base_recalibrator.xml @ 22:bc18c5ad280f draft

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Remove thread options from base_recalibrator.xml
author Jim Johnson <jj@umn.edu>
date Fri, 28 Dec 2012 12:08:47 -0600
parents 6e641ee02851
children 2f9bf8bf42b7
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line diff
--- a/base_recalibrator.xml	Fri Dec 28 11:50:20 2012 -0600
+++ b/base_recalibrator.xml	Fri Dec 28 12:08:47 2012 -0600
@@ -15,7 +15,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "BaseRecalibrator"
     \$GATK2_SITE_OPTIONS
-    \$GATK2_THREAD_OPTIONS
+    ## \$GATK2_THREAD_OPTIONS
     ##--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