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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
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corin 2011-02-03 18:33:29 +00:00
parent 9fc45e1234
commit a22ea53665
1 changed files with 4 additions and 4 deletions
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8
shell/queue.sh
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@ -1,10 +1,10 @@
#!/bin/sh
SAMPLE_SET=$1
STING_HOME=/humgen/gsa-firehose2/pipeline/repositories/StingProduction
STING_HOME=/humgen/gsa-pipeline/.repository
REFSEQ_TABLE=/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg19.txt
JOB_QUEUE=gsa
SHORT_QUEUE=gsa
JOB_QUEUE=week
SHORT_QUEUE=hour
TMP_DIR=$PWD/tmp
mkdir $PWD/tmp
@ -14,4 +14,4 @@ use R-2.10
use Oracle-full-client
use .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
java -Djava.io.tmpdir="$TMP_DIR" -jar "$STING_HOME"/dist/Queue.jar -jobQueue "$JOB_QUEUE" -shortJobQueue "$SHORT_QUEUE" -jobProject "$SAMPLE_SET" -jobPrefix "$SAMPLE_SET" -tearScript ~/Sting/R/DataProcessingReport/GetTearsheetStats.R -S ~/Sting/scala/qscript/fullCallingPipeline.q -Y "$SAMPLE_SET".yaml -refseqTable "$REFSEQ_TABLE" --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -log queue_log.txt -statusTo corin -bsub $2
java -Djava.io.tmpdir="$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 -refseqTable "$REFSEQ_TABLE" --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -log queue_log.txt -statusTo corin -bsub $2