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comparison depth_of_coverage.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
15 #end for 15 #end for
16 -p 'java 16 -p 'java
17 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" 17 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
18 -T "DepthOfCoverage" 18 -T "DepthOfCoverage"
19 \$GATK2_SITE_OPTIONS 19 \$GATK2_SITE_OPTIONS
20 \$GATK2_THREAD_OPTIONS 20 ## \$GATK2_NUM_THREADS
21 ##--num_threads 4 ##hard coded, for now 21 ##--num_threads 4 ##hard coded, for now
22
23 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home 22 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
24 #if $reference_source.reference_source_selector != "history": 23 #if $reference_source.reference_source_selector != "history":
25 -R "${reference_source.ref_file.fields.path}" 24 -R "${reference_source.ref_file.fields.path}"
26 #end if 25 #end if
27 #if str( $input_calculate_coverage_over_genes ) != "None": 26 #if str( $input_calculate_coverage_over_genes ) != "None":