#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.1583c778" && echo "/cromwell_root/tmp.1583c778")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
outd2cdaeae="${tmpDir}/out.$$" errd2cdaeae="${tmpDir}/err.$$"
mkfifo "$outd2cdaeae" "$errd2cdaeae"
trap 'rm "$outd2cdaeae" "$errd2cdaeae"' EXIT
tee '/cromwell_root/stdout' < "$outd2cdaeae" &
tee '/cromwell_root/stderr' < "$errd2cdaeae" >&2 &
(
cd /cromwell_root


set -euo pipefail

unzip /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/038fcf2f-32c7-437e-beb7-ded16a017a25/correlate_genomic_events_all/d2cdaeae-8d2e-46f5-b7bd-6cd908ffe652/call-correlate_genomic_event_clinical/correlate_genomic_event_clinical.zip -d `dirname /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/038fcf2f-32c7-437e-beb7-ded16a017a25/correlate_genomic_events_all/d2cdaeae-8d2e-46f5-b7bd-6cd908ffe652/call-correlate_genomic_event_clinical/analysis.results.RData`

Rscript /src/GDAC_Correlate_Genomic_Events_NozzleReport.R \
--libdir "/src" \
--rdataFilename /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/038fcf2f-32c7-437e-beb7-ded16a017a25/correlate_genomic_events_all/d2cdaeae-8d2e-46f5-b7bd-6cd908ffe652/call-correlate_genomic_event_clinical/analysis.results.RData \
--geneEvent CLUS_CNVARM 

zip -D report.zip * -x exec.sh

if true; then
	mv /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/038fcf2f-32c7-437e-beb7-ded16a017a25/correlate_genomic_events_all/d2cdaeae-8d2e-46f5-b7bd-6cd908ffe652/call-correlate_genomic_event_clinical/correlate_genomic_events_all.zip .
	zip -r correlate_genomic_events_all.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
)  > "$outd2cdaeae" 2> "$errd2cdaeae"
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
