18 lines
816 B
Bash
Executable File
18 lines
816 B
Bash
Executable File
#!/bin/sh
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SAMPLE_SET=$1
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STING_HOME=/humgen/gsa-firehose2/pipeline/repositories/StingProduction
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REFSEQ_TABLE=/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg19.txt
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JOB_QUEUE=gsa
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SHORT_QUEUE=gsa
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TMP_DIR=$PWD/tmp
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mkdir $PWD/tmp
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source /broad/software/scripts/useuse
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use LSF
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use R-2.10
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use Oracle-full-client
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use .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
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java -Djava.io.tmpdir="$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
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