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comparison base_recalibrator.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 6460f2ba6a60
children b99c25b0ad4d
comparison
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27:b23ecdd665d0 28:6ef8eb568700
13 #end if 13 #end if
14 -p 'java 14 -p 'java
15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
16 -T "BaseRecalibrator" 16 -T "BaseRecalibrator"
17 \$GATK2_SITE_OPTIONS 17 \$GATK2_SITE_OPTIONS
18 ## \$GATK2_THREAD_OPTIONS 18 \$GATK2_CPU_THREADS
19 ##--num_threads 4 ##hard coded, for now 19 ##--num_threads 4 ##hard coded, for now
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 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout 21 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
22 #if $reference_source.reference_source_selector != "history": 22 #if $reference_source.reference_source_selector != "history":
23 -R "${reference_source.ref_file.fields.path}" 23 -R "${reference_source.ref_file.fields.path}"