# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1352225256 21600
# Node ID a14e79e7ac758a39593344dd34c025ef6e9d409d
# Parent  24504f5cac5e7b2a21a575acf3b3dc5bd7ae6e9f
Comment out site options from reduce_reads.xml

diff -r 24504f5cac5e -r a14e79e7ac75 reduce_reads.xml
--- 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