Mercurial > repos > jjohnson > gatk2

comparison indel_realigner.xml @ 20:3924f62cd4e7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
19:d1a88bdaa80a 20:3924f62cd4e7
14 -p 'java 14 -p 'java
15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
16 -T "IndelRealigner" 16 -T "IndelRealigner"
17 -o "${output_bam}" 17 -o "${output_bam}"
18 \$GATK2_SITE_OPTIONS 18 \$GATK2_SITE_OPTIONS
19 \$GATK2_THREAD_OPTIONS 19 ## \$GATK2_THREAD_OPTIONS
20 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home 20 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
21 ##--num_threads 4 ##hard coded, for now 21 ##--num_threads 4 ##hard coded, for now
22 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout 22 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
23 #if $reference_source.reference_source_selector != "history": 23 #if $reference_source.reference_source_selector != "history":
24 -R "${reference_source.ref_file.fields.path}" 24 -R "${reference_source.ref_file.fields.path}"