#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.a150bf9f" && echo "/cromwell_root/tmp.a150bf9f")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
outd44c315a="${tmpDir}/out.$$" errd44c315a="${tmpDir}/err.$$"
mkfifo "$outd44c315a" "$errd44c315a"
trap 'rm "$outd44c315a" "$errd44c315a"' EXIT
tee '/cromwell_root/stdout' < "$outd44c315a" &
tee '/cromwell_root/stderr' < "$errd44c315a" >&2 &
(
cd /cromwell_root


Rscript /src/aggregate_clusters.R \
	 \
	--mRNAhc /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/5c10a466-2c55-4142-af9c-5979dff38175/clustering_hierarchical/9cb182e8-60c0-4c2d-ae27-c5f55ad25c11/call-cluster_select_best/CPTAC3-LUAD-TP.bestclus.txt \
	 \
	--lincRNAhc /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/7452fc12-57b1-43cf-a11e-5e8b2d123a69/clustering_hierarchical/a92c63ca-2a74-434a-831c-ca43fbd43a96/call-cluster_select_best/CPTAC3-LUAD-TP.bestclus.txt \
	 \
	 \
	 \
	 \
	 \
	 \
	 \
	 \
	 \
	 \
	--outputPrefix CPTAC3-LUAD-TP \
	 \
	

if true
	then zip -r aggregate_clusters . -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
)  > "$outd44c315a" 2> "$errd44c315a"
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
