Mercurial > repos > jjohnson > gatk2
diff 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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--- a/reduce_reads.xml Mon Feb 18 11:17:32 2013 -0600 +++ b/reduce_reads.xml Mon Feb 18 15:48:46 2013 -0600 @@ -16,7 +16,7 @@ -T "ReduceReads" -o "${output_bam}" ## \$GATK2_SITE_OPTIONS - ## \$GATK2_THREAD_OPTIONS + ## \$GATK2_NUM_THREADS ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home ##--num_threads 4 ##not supported yet ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout