69 lines
1.9 KiB
Bash
Executable File
69 lines
1.9 KiB
Bash
Executable File
#!/bin/sh
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# Downloads a set of samples from Firehose using the obsolete Firehose Test Harness and generate a TSV file with the outputs.
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ENTITY_SET_ID=$1
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ENTITY_SET_TYPE=Sample_Set
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ENTITY_TYPE=Sample
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if [ "$ENTITY_SET_ID" == "" ]; then
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echo "Usage: $0 <Sample_Set_Name>" >&2
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exit 1
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fi
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# Firehose variables
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FIREHOSE_SOURCE_HOME=/humgen/gsa-firehose/firehose/source
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CGA_HOME=$FIREHOSE_SOURCE_HOME/CancerGenomeAnalysis
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FIREHOSE_TEST_HARNESS="python $CGA_HOME/analysis_pipeline/scripts/firehose_test_harness.py"
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FIREHOSE_HOST=firehose
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FIREHOSE_PORT=8080
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FIREHOSE_DOMAIN=gsa
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FIREHOSE_WORKSPACE=trunk
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# TSV file to write
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PIPELINE_TSV_FILE=$ENTITY_SET_ID.tsv
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# Annotations to pull down from Firehose
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FIREHOSE_ANNOTATIONS=(reference_file interval_list sample_id recalibrated_bam_file squid_project collaborator_id)
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index=0
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count=${#FIREHOSE_ANNOTATIONS[@]}
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TSV_HEADER=""
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FIREHOSE_VARIABLES=""
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TAB=' '
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# Build the tab separated list of firehose arguments
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while [ "$index" -lt "$count" ]; do
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if [ "$FIREHOSE_VARIABLES" != "" ]; then
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FIREHOSE_VARIABLES=$FIREHOSE_VARIABLES$TAB
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TSV_HEADER=$TSV_HEADER$TAB
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fi
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FIREHOSE_VARIABLES=$FIREHOSE_VARIABLES'${'${FIREHOSE_ANNOTATIONS[$index]}'}'
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TSV_HEADER=$TSV_HEADER${FIREHOSE_ANNOTATIONS[$index]}
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let "index = $index + 1"
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done
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# Retrieve all the required variables via the test harness.
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$FIREHOSE_TEST_HARNESS \
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-d $FIREHOSE_DOMAIN -w $FIREHOSE_WORKSPACE \
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-t $ENTITY_TYPE -f $ENTITY_SET_ID -y $ENTITY_SET_TYPE \
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"echo '$FIREHOSE_VARIABLES'" && \
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\
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# Generate tsv header
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echo "$TSV_HEADER" > $PIPELINE_TSV_FILE \
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# Generate tsv from firehose output
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. firehose-populated-commands.sh >> $PIPELINE_TSV_FILE
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EXIT_CODE=$?
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if [[ $EXIT_CODE -ne 0 ]]; then
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echo "" >&2
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echo "The Firehose test harness failed with exit code:" $EXIT_CODE >&2
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echo 'Check the name of your Sample_Set or try using the newer getFirehoseCurlTsv.sh' >&2
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exit $EXIT_CODE
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fi
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