Mercurial > repos > jjohnson > gatk2
changeset 22:bc18c5ad280f draft
Remove thread options from base_recalibrator.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 28 Dec 2012 12:08:47 -0600 |
| parents | 6e641ee02851 |
| children | 2f9bf8bf42b7 |
| files | base_recalibrator.xml |
| diffstat | 1 files changed, 1 insertions(+), 1 deletions(-) [+] |
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--- a/base_recalibrator.xml Fri Dec 28 11:50:20 2012 -0600 +++ b/base_recalibrator.xml Fri Dec 28 12:08:47 2012 -0600 @@ -15,7 +15,7 @@ -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" -T "BaseRecalibrator" \$GATK2_SITE_OPTIONS - \$GATK2_THREAD_OPTIONS + ## \$GATK2_THREAD_OPTIONS ##--num_threads 4 ##hard coded, for now ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout