Mercurial > repos > jjohnson > gatk2

diff reduce_reads.xml @ 10:a14e79e7ac75 draft

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Comment out site options from reduce_reads.xml
author Jim Johnson <jj@umn.edu>
date Tue, 06 Nov 2012 12:07:36 -0600
parents f253357915e0
children 5faf7ace8aee
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--- a/reduce_reads.xml	Tue Nov 06 11:48:49 2012 -0600
+++ b/reduce_reads.xml	Tue Nov 06 12:07:36 2012 -0600
@@ -15,7 +15,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "ReduceReads"
     -o "${output_bam}"
-    \$GATK2_SITE_OPTIONS
+    ## \$GATK2_SITE_OPTIONS
     ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
     ##--num_threads 4 ##not supported yet
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout