93 lines
2.1 KiB
Bash
93 lines
2.1 KiB
Bash
#!/bin/sh
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# Downloads a set of samples from Firehose using the Firehose Test Harness and awk to generate a YAML file.
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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 $CGA_HOME/analysis_pipeline/scripts/firehose_test_harness.py"
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FIREHOSE_HOST=firehose
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FIREHOSE_PORT=8080
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FIREHOSE_DOMAIN=gsa
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FIREHOSE_WORKSPACE=trunk
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# YAML file to write
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PIPELINE_YAML_FILE=$ENTITY_SET_ID.yaml
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# Annotations to pull down from Firehose
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FIREHOSE_ANNOTATIONS=(reference_file dbsnp_file interval_list \
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sample_id recalibrated_bam_file squid_project collaborator_id)
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# YAML templates
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PROJECT_YAML_TEMPLATE='" \
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project: { \
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name: '"$ENTITY_SET_ID"', \
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referenceFile: %s, \
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dbsnpFile: %s, \
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intervalList: %s \
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},", $1, $2, $3'
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SAMPLE_YAML_TEMPLATE='" \
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{ \
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id: %s, \
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bamFiles: { recalibrated: %s }, \
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tags: { \
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SQUIDProject: %s, \
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CollaboratorID: %s \
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} \
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}", $4, $5, $6, $7'
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index=0
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count=${#FIREHOSE_ANNOTATIONS[@]}
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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$TAB
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fi
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FIREHOSE_VARIABLES=$FIREHOSE_VARIABLES'${'${FIREHOSE_ANNOTATIONS[$index]}'}'
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let "index = $index + 1"
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done
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# Retrieve all the required variables and run the pipeline in Queue.
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$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 yaml from firehose output
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. firehose-populated-commands.sh | awk '
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BEGIN {
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printf "{"
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}
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{
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if (NR == 1) {
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printf '"$PROJECT_YAML_TEMPLATE"'
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printf "\n samples: ["
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} else {
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printf ","
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}
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printf '"$SAMPLE_YAML_TEMPLATE"'
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}
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END {
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if (NR > 0)
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printf "\n ]"
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print "\n}"
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}' > $PIPELINE_YAML_FILE
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