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gatk-3.8/shell/queue.sh

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An example template for the shell script used to run the full calling pipeline on the broad system git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5022 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 04:28:59 +08:00
#!/bin/sh
SAMPLE_SET=$1
Updated template for the MPG pipeline's queue script runner. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5187 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 02:33:29 +08:00
STING_HOME=/humgen/gsa-pipeline/.repository
JOB_QUEUE=week
SHORT_QUEUE=hour
An example template for the shell script used to run the full calling pipeline on the broad system git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5022 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 04:28:59 +08:00
TMP_DIR=$PWD/tmp
mkdir $PWD/tmp
source /broad/software/scripts/useuse
use LSF
use R-2.10
use Oracle-full-client
use .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp. Added a genotypeDbsnpType and evalDbsnpType to check the extensions for .vcf or .rod. Moved renaming of "recalibrated" bams to "cleaned" from sed to yaml generation template (see diff for more info). Renamed fCP.q to FCP.q. Though it's still disabled until VariantEval is updated, added changes above to the FCPTest. Removed refseq table from the queue.sh wrapper script. Only specified in the yaml. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5213 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 06:01:09 +08:00
java -Djava.io.tmpdir="$TMP_DIR" -jar "$STING_HOME"/dist/Queue.jar -jobQueue "$JOB_QUEUE" -shortJobQueue "$SHORT_QUEUE" -jobProject "$SAMPLE_SET" -jobPrefix "$SAMPLE_SET" -tearScript "$STING_HOME"/R/DataProcessingReport/GetTearsheetStats.R -S "$STING_HOME"/scala/qscript/playground/FullCallingPipeline.q -Y "$SAMPLE_SET".yaml --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -log queue_log.txt -statusTo corin -bsub $2