diff --git a/shell/queue.sh b/shell/queue.sh index d95b55425..a939f5525 100755 --- a/shell/queue.sh +++ b/shell/queue.sh @@ -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