# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1356715300 21600
# Node ID 3924f62cd4e75528e3b7474e01cf65b0f65c675b
# Parent  d1a88bdaa80a50e39e066bb9466e2adc317faf88
remove thread options from indel_realigner.xml

diff -r d1a88bdaa80a -r 3924f62cd4e7 indel_realigner.xml
--- 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