#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.af2f4525" && echo "/cromwell_root/tmp.af2f4525")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
outabf2ca5c="${tmpDir}/out.$$" errabf2ca5c="${tmpDir}/err.$$"
mkfifo "$outabf2ca5c" "$errabf2ca5c"
trap 'rm "$outabf2ca5c" "$errabf2ca5c"' EXIT
tee '/cromwell_root/stdout' < "$outabf2ca5c" &
tee '/cromwell_root/stderr' < "$errabf2ca5c" >&2 &
(
cd /cromwell_root


set -euo pipefail

unzip /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/069a11b4-7b1a-48bc-8231-942ea7a19e7c/correlate_genomic_events_all/abf2ca5c-bd5f-4d49-8b37-7914065d06a1/call-correlate_genomic_event_clinical/correlate_genomic_event_clinical.zip -d `dirname /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/069a11b4-7b1a-48bc-8231-942ea7a19e7c/correlate_genomic_events_all/abf2ca5c-bd5f-4d49-8b37-7914065d06a1/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/069a11b4-7b1a-48bc-8231-942ea7a19e7c/correlate_genomic_events_all/abf2ca5c-bd5f-4d49-8b37-7914065d06a1/call-correlate_genomic_event_clinical/analysis.results.RData \
--geneEvent CLI_CNVARM 

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

if true; then
	mv /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/069a11b4-7b1a-48bc-8231-942ea7a19e7c/correlate_genomic_events_all/abf2ca5c-bd5f-4d49-8b37-7914065d06a1/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
)  > "$outabf2ca5c" 2> "$errabf2ca5c"
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
