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comparison variant_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 7533db8dfb5b
children a5c55503d196
comparison
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27:b23ecdd665d0 28:6ef8eb568700
11 #end for 11 #end for
12 -p 'java 12 -p 'java
13 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 13 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
14 -T "VariantRecalibrator" 14 -T "VariantRecalibrator"
15 \$GATK2_SITE_OPTIONS 15 \$GATK2_SITE_OPTIONS
16 \$GATK2_THREAD_OPTIONS 16 \$GATK2_NUM_THREADS
17 ##--num_threads 4 ##hard coded, for now 17 ##--num_threads 4 ##hard coded, for now
18 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file"##ET no phone home 18 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file"##ET no phone home
19 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout 19 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
20 #if $reference_source.reference_source_selector != "history": 20 #if $reference_source.reference_source_selector != "history":
21 -R "${reference_source.ref_file.fields.path}" 21 -R "${reference_source.ref_file.fields.path}"