Mercurial > repos > jjohnson > gatk2
comparison variant_eval.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> |
|---|---|
| date | Mon, 18 Feb 2013 15:48:46 -0600 |
| parents | 7533db8dfb5b |
| children | 76f8ca47b810 |
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| 27:b23ecdd665d0 | 28:6ef8eb568700 |
|---|---|
| 13 -p 'java | 13 -p 'java |
| 14 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" | 14 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" |
| 15 -T "VariantEval" | 15 -T "VariantEval" |
| 16 --out "${output_report}" | 16 --out "${output_report}" |
| 17 \$GATK2_SITE_OPTIONS | 17 \$GATK2_SITE_OPTIONS |
| 18 \$GATK2_THREAD_OPTIONS | 18 \$GATK2_NUM_THREADS |
| 19 ##--num_threads 4 ##hard coded, for now | 19 ##--num_threads 4 ##hard coded, for now |
| 20 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home | 20 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home |
| 21 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout | 21 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout |
| 22 #if $reference_source.reference_source_selector != "history": | 22 #if $reference_source.reference_source_selector != "history": |
| 23 -R "${reference_source.ref_file.fields.path}" | 23 -R "${reference_source.ref_file.fields.path}" |