diff --git a/shell/queue.sh b/shell/queue.sh new file mode 100755 index 000000000..278137387 --- /dev/null +++ b/shell/queue.sh @@ -0,0 +1,18 @@ +#!/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