17 lines
693 B
Bash
Executable File
17 lines
693 B
Bash
Executable File
#!/bin/sh
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SAMPLE_SET=$1
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STING_HOME=/humgen/gsa-pipeline/.repository
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JOB_QUEUE=week
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SHORT_QUEUE=hour
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TMP_DIR=$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_HOME"/R/DataProcessingReport/GetTearsheetStats.R -S "$STING_HOME"/scala/qscript/playground/FullCallingPipeline.q -Y "$SAMPLE_SET".yaml --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -log queue_log.txt -statusTo corin -bsub $2
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