85 lines
3.0 KiB
Bash
Executable File
85 lines
3.0 KiB
Bash
Executable File
#!/bin/sh
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ENTITY_TYPE=$1
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ENTITY_ID=$2
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FIREHOSE_TOKEN=$3
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FIREHOSE_WORKSPACE=trunk
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FIREHOSE_HOST=firehose
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FIREHOSE_PORT=8080
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FIREHOSE_DOMAIN=gsa
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CLEAN_BAM_ANNOTATION=clean_bam_file
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DEFAULT_QUEUE=gsa
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SHORT_QUEUE=hour
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FIREHOSE_SOURCE_HOME=/humgen/gsa-firehose/firehose/source
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STING_HOME=$FIREHOSE_SOURCE_HOME/Sting
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CGA_HOME=$FIREHOSE_SOURCE_HOME/CancerGenomeAnalysis
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RUN=-run
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TMP_DIR=/broad/shptmp/$USER
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JOB_QUEUE=gsa
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INTERVAL_COUNT=15
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REALIGNER_COUNT=50
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QUEUE_JAR=$STING_HOME/dist/Queue.jar
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GATK_JAR=$STING_HOME/dist/GenomeAnalysisTK.jar
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FIX_MATES_JAR=/seq/software/picard/1.194/bin/FixMateInformation.jar
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SAMTOOLS=/seq/dirseq/samtools/samtools-0.1.7-5/samtools
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FIREHOSE_IMPORT_JAR=$CGA_HOME/analysis_pipeline/tools/dist/ImportSingleValue.jar
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CLEAN_BAM_FILE_SCRIPT=$STING_HOME/scala/qscript/kshakir/CleanBamFile.scala
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FIREHOSE_TEST_HARNESS="python $CGA_HOME/analysis_pipeline/scripts/firehose_test_harness.py"
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SPLIT_BY_CONTIG="python $STING_HOME/python/splitIntervalsByContig.py"
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SPLIT_BY_INTERVALS=$STING_HOME/shell/splitIntervals.sh
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MERGE_TEXT=$STING_HOME/shell/mergeText.sh
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CONVERT_BLACKLIST=$CGA_HOME/analysis_pipeline/genepattern/modules/ConvertDependentsList/convert_dependents_list.sh
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# Record the Sting version number.
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svnversion $STING_HOME > stingversion.txt
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# If Sting has been modified, record the differences.
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grep -E '^[0-9]+$' stingversion.txt || svn diff $STING_HOME > stingdiff.txt
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# Record the CGA version number.
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svnversion $CGA_HOME > cgaversion.txt
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# If CGA has been modified, record the differences.
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grep -E '^[0-9]+$' cgaversion.txt || svn diff $CGA_HOME > cgadiff.txt
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# Try to retrieve the blacklist. If it fails then set it to "".
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$FIREHOSE_TEST_HARNESS -d $FIREHOSE_DOMAIN -w $FIREHOSE_WORKSPACE -n $ENTITY_ID -t $ENTITY_TYPE 'BLACKLIST="${read_group_blacklist}"' && . firehose-populated-commands.sh || BLACKLIST=""
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# Retrieve all the required variables and run the pipeline in Queue.
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$FIREHOSE_TEST_HARNESS -d $FIREHOSE_DOMAIN -w $FIREHOSE_WORKSPACE -n $ENTITY_ID -t $ENTITY_TYPE 'REFERENCE_FILE="${reference_file}";BAM_FILE="${recalibrated_bam_file}";DBSNP_FILE="${dbsnp_file}";INTERVAL_FILE="${interval_list}";DATABASE_ID="${database_id}"' && . firehose-populated-commands.sh && \
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\
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JOB_PREFIX=Q-$ENTITY_ID && \
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\
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java \
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-Djava.io.tmpdir="$TMP_DIR" \
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-jar "$QUEUE_JAR" \
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-S "$CLEAN_BAM_FILE_SCRIPT" \
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-bsub -bsubWait -skipUpToDate \
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-jobQueue "$JOB_QUEUE" \
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-jobPrefix "$JOB_PREFIX" \
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-gatk "$GATK_JAR" \
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-base "$ENTITY_ID" \
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-R "$REFERENCE_FILE" \
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-I "$BAM_FILE" \
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-D "$DBSNP_FILE" \
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-L "$INTERVAL_FILE" \
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-RTCSS "$SPLIT_BY_CONTIG" \
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-RTCSC "$INTERVAL_COUNT" \
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-IRSS "$SPLIT_BY_INTERVALS" \
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-IRSC "$REALIGNER_COUNT" \
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-MTS "$MERGE_TEXT" \
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-fixMates "$FIX_MATES_JAR" \
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-samtools "$SAMTOOLS" \
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-RGBLS "$CONVERT_BLACKLIST" \
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-RGBL "$BLACKLIST" \
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-importJar "$FIREHOSE_IMPORT_JAR" \
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-shortQueue "$SHORT_QUEUE" \
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-FHHost "$FIREHOSE_HOST" \
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-FHPort "$FIREHOSE_PORT" \
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-FHDomain "$FIREHOSE_DOMAIN" \
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-FHToken "$FIREHOSE_TOKEN" \
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-bamFHEType "$ENTITY_TYPE" \
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-bamFHEID "$DATABASE_ID" \
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-bamFHAnn "$CLEAN_BAM_ANNOTATION" \
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$RUN || ( echo Job failed. Check stdout.txt for more info. >&2; exit 1; )
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