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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
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corin 2011-01-19 20:28:59 +00:00
parent dfcd45181a
commit af60666f5d
1 changed files with 18 additions and 0 deletions
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shell/queue.sh 100755
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#!/bin/sh
SAMPLE_SET=$1
STING_HOME=/humgen/gsa-firehose2/pipeline/repositories/StingProduction
REFSEQ_TABLE=/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg19.txt
JOB_QUEUE=gsa
SHORT_QUEUE=gsa
BIG_QUEUE=gsa
TMP_DIR=$PWD/tmp
mkdir $PWD/tmp
source /broad/software/scripts/useuse
use LSF
use R-2.10
use Oracle-full-client
use .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
java -Djava.io.tmpdir="$TMP_DIR" -jar "$STING_HOME"/dist/Queue.jar -jobQueue "$JOB_QUEUE" -shortJobQueue "$SHORT_QUEUE" -bigMemQueue "$BIG_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