#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.565c9c06" && echo "/cromwell_root/tmp.565c9c06")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
outeef2971f="${tmpDir}/out.$$" erreef2971f="${tmpDir}/err.$$"
mkfifo "$outeef2971f" "$erreef2971f"
trap 'rm "$outeef2971f" "$erreef2971f"' EXIT
tee '/cromwell_root/stdout' < "$outeef2971f" &
tee '/cromwell_root/stderr' < "$erreef2971f" >&2 &
(
cd /cromwell_root


RunR.sh /src/ClinicalAnalysisAllGenesReport_nozzle.R /src  -iR/cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/7e5c0b4f-e849-41ec-a1f1-6255d4b3b676/correlate_clinical_vs_expression/eef2971f-420b-4233-9785-5a33253582e7/call-correlate_expression_clinical/clinical-results.txt -iI/cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/7e5c0b4f-e849-41ec-a1f1-6255d4b3b676/correlate_clinical_vs_expression/eef2971f-420b-4233-9785-5a33253582e7/call-correlate_expression_clinical/clinical-results.RData -rN10 -cP0.05 -cQ0.3 -OPMUTATION_RATE  
zip -r report.zip .
if true; then
	mv /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/7e5c0b4f-e849-41ec-a1f1-6255d4b3b676/correlate_clinical_vs_expression/eef2971f-420b-4233-9785-5a33253582e7/call-correlate_expression_clinical/correlate_clinical_vs_expression.zip .
	zip -r correlate_clinical_vs_expression.zip . -x \
		"fc-[a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9]/*" \
		lost+found/\* \
		broad-institute-gdac/\* \
		"tmp.[a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9]/*" \
		exec.sh \
		report.zip
fi
)  > "$outeef2971f" 2> "$erreef2971f"
echo $? > /cromwell_root/rc.tmp
(
# add a .file in every empty directory to facilitate directory delocalization on the cloud
cd /cromwell_root
find . -type d -exec sh -c '[ -z "$(ls -A '"'"'{}'"'"')" ] && touch '"'"'{}'"'"'/.file' \;
)
(
cd /cromwell_root
sync


)
mv /cromwell_root/rc.tmp /cromwell_root/rc
