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comparison indel_realigner.xml @ 28:6ef8eb568700 draft

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Move GATK tool_dependency to a repository dependency, use 2 env vars: GATK2_NUM_THREADS and GATK2_NUM_CPU_THREADS for site threading values
author Jim Johnson <jj@umn.edu>
date Mon, 18 Feb 2013 15:48:46 -0600
parents 3924f62cd4e7
children 76f8ca47b810
comparison
equal deleted inserted replaced
27:b23ecdd665d0 28:6ef8eb568700
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_NUM_THREADS
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}"