#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.b012ec8e" && echo "/cromwell_root/tmp.b012ec8e")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
out56785d48="${tmpDir}/out.$$" err56785d48="${tmpDir}/err.$$"
mkfifo "$out56785d48" "$err56785d48"
trap 'rm "$out56785d48" "$err56785d48"' EXIT
tee '/cromwell_root/stdout' < "$out56785d48" &
tee '/cromwell_root/stderr' < "$err56785d48" >&2 &
(
cd /cromwell_root


set -euo pipefail

# Generate file of localized stick figure paths
if true; then
	cp /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_stick_figures/headers.txt generatedStickFigurePaths.txt
	sort /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_stick_figures/SIGNIFICANT_GENE.txt > stick_figure_genes.txt
	sort /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-report_mutsig/write_lines_cb1e6a40d76dd3f06b567d784e516e51.tmp > stick_figure_txt.txt
	sort /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-report_mutsig/write_lines_7985a7c5ebef307f44596f76338d1c79.tmp > stick_figure_jpg.txt
	sort /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-report_mutsig/write_lines_ad45095bea362eb2ccdb69af5711fb53.tmp > stick_figure_pdf.txt
	paste stick_figure_genes.txt \
		  stick_figure_txt.txt \
		  stick_figure_jpg.txt \
		  stick_figure_pdf.txt \
	>> generatedStickFigurePaths.txt
fi

/src/Mutsig_Report.R \
	 \
	 \
	--categories_table_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_mutsig2cv/cacheCopy/mutcategs.txt \
	 \
	 \
	 \
	 \
	 \
	 \
	--patients_counts_rates_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_mutsig2cv/cacheCopy/patient_counts_and_rates.txt \
	--coMut_plot_png_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_comut/PanCan_coMut.png \
	--coMut_plot_pdf_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_comut/PanCan_coMut.pdf \
	--stick_figures_path generatedStickFigurePaths.txt \
	--maf_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_mutsig2cv/cacheCopy/PanCan.final_analysis_set.maf \
	 \
	 \
	--lego_plotter_mut_profile_png_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_lego_plotter/cacheCopy/PanCan.final_analysis_set.maf.mutation_profile.png \
	--lego_plotter_mut_profile_AF_png_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_lego_plotter/cacheCopy/PanCan.final_analysis_set.maf.mutation_profile_AF.png \
	--lego_plotter_mut_profile_ai_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_lego_plotter/cacheCopy/PanCan.final_analysis_set.maf.mutation_profile.ai \
	--lego_plotter_mut_profile_AF_ai_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_lego_plotter/cacheCopy/PanCan.final_analysis_set.maf.mutation_profile_AF.ai \
	PanCan /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_mutsig2cv/cacheCopy/sig_genes.txt /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_mutsig2cv/cacheCopy/MutSig_version.txt

if true; then
	cat /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_mutsig2cv/cacheCopy/tool_mutsig2cv.zip /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_comut/tool_comut.zip /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_lego_plotter/cacheCopy/tool_lego_plotter.zip /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/29cdcd1a-4780-4881-99d8-25788b1a305f/mutation_mutsig2cv/56785d48-396f-4360-8629-f1a603461a1f/call-tool_stick_figures/tool_stick_figures.zip > tmp.zip
	zip -FF tmp.zip --out report_mutsig.zip > /dev/null 2>&1
	rm tmp.zip
	zip -r report_mutsig.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]/*" \
		"fc-secure-[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][a-zA-Z0-9][a-zA-Z0-9]/*" \
		exec.sh \
		generatedStickFigurePaths.txt \
		stick_figure_\*.txt
fi
)  > "$out56785d48" 2> "$err56785d48"
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