Mercurial > repos > jjohnson > gatk2

diff indel_realigner.xml @ 20:3924f62cd4e7 draft

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remove thread options from indel_realigner.xml
author Jim Johnson <jj@umn.edu>
date Fri, 28 Dec 2012 11:21:40 -0600
parents 7533db8dfb5b
children 6ef8eb568700
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--- a/indel_realigner.xml	Fri Dec 28 11:08:23 2012 -0600
+++ b/indel_realigner.xml	Fri Dec 28 11:21:40 2012 -0600
@@ -16,7 +16,7 @@
     -T "IndelRealigner"
     -o "${output_bam}"
     \$GATK2_SITE_OPTIONS
-    \$GATK2_THREAD_OPTIONS
+    ## \$GATK2_THREAD_OPTIONS
     ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
     ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout