#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.3df6300b" && echo "/cromwell_root/tmp.3df6300b")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
out4f214c4b="${tmpDir}/out.$$" err4f214c4b="${tmpDir}/err.$$"
mkfifo "$out4f214c4b" "$err4f214c4b"
trap 'rm "$out4f214c4b" "$err4f214c4b"' EXIT
tee '/cromwell_root/stdout' < "$out4f214c4b" &
tee '/cromwell_root/stderr' < "$err4f214c4b" >&2 &
(
cd /cromwell_root


RunR.sh /src/ClinicalAnalysisAllGenesReport_nozzle.R /src  -iR/cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/4f266055-3350-4131-baac-9594721b5488/correlate_clinical_vs_expression/4f214c4b-4adc-4efb-9bad-39703636aae2/call-correlate_expression_clinical/clinical-results.txt -iI/cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/4f266055-3350-4131-baac-9594721b5488/correlate_clinical_vs_expression/4f214c4b-4adc-4efb-9bad-39703636aae2/call-correlate_expression_clinical/clinical-results.RData -rN10 -cP0.05 -cQ0.3 -OPAPOBEC  
zip -r report.zip .
if true; then
	mv /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/4f266055-3350-4131-baac-9594721b5488/correlate_clinical_vs_expression/4f214c4b-4adc-4efb-9bad-39703636aae2/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
)  > "$out4f214c4b" 2> "$err4f214c4b"
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
