Mercurial > repos > jjohnson > gatk2
comparison reduce_reads.xml @ 28:6ef8eb568700 draft
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> |
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date | Mon, 18 Feb 2013 15:48:46 -0600 |
parents | 7533db8dfb5b |
children | 76f8ca47b810 |
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27:b23ecdd665d0 | 28:6ef8eb568700 |
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14 -p 'java | 14 -p 'java |
15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" | 15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" |
16 -T "ReduceReads" | 16 -T "ReduceReads" |
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 ##not supported yet | 21 ##--num_threads 4 ##not supported yet |
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}" |