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comparison variant_combine.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 7533db8dfb5b
children 76f8ca47b810
comparison
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27:b23ecdd665d0 28:6ef8eb568700
17 -p 'java 17 -p 'java
18 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 18 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
19 -T "CombineVariants" 19 -T "CombineVariants"
20 --out "${output_variants}" 20 --out "${output_variants}"
21 \$GATK2_SITE_OPTIONS 21 \$GATK2_SITE_OPTIONS
22 \$GATK2_THREAD_OPTIONS 22 \$GATK2_NUM_THREADS
23 ##--num_threads 4 ##hard coded, for now 23 ##--num_threads 4 ##hard coded, for now
24 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home 24 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
25 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout 25 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
26 #if $reference_source.reference_source_selector != "history": 26 #if $reference_source.reference_source_selector != "history":
27 -R "${reference_source.ref_file.fields.path}" 27 -R "${reference_source.ref_file.fields.path}"