#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.2fbfd02f" && echo "/cromwell_root/tmp.2fbfd02f")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
out68755938="${tmpDir}/out.$$" err68755938="${tmpDir}/err.$$"
mkfifo "$out68755938" "$err68755938"
trap 'rm "$out68755938" "$err68755938"' EXIT
tee '/cromwell_root/stdout' < "$out68755938" &
tee '/cromwell_root/stderr' < "$err68755938" >&2 &
(
cd /cromwell_root


Rscript --vanilla /src/CN_postprocess.R -c /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/b6064b6c-6bfd-4c61-986b-9864aac7a226/copy_number_gistic2/dabe62b3-9ee9-4644-b01c-ae86d498dd18/call-tool_gistic2/all_lesions.txt -o CPTAC3-LUAD-TP
if true
	then zip -r tool_gistic2_postprocess . -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
fi
)  > "$out68755938" 2> "$err68755938"
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
