SINGE.sh

#!/bin/bash
# Bash script to run compiled MATLAB code
# Requires MATLAB runtime library which can be downloaded from
# https://www.mathworks.com/products/compiler/matlab-runtime.html
# 
# Example:
# bash SINGE.sh PATH_TO_RUNTIME standalone data1/X_SCODE_data.mat data1/gene_list.mat Output data1/default_hyperparameters.txt

usage="Usage: $(basename $0) runtime_dir mode Data gene_list outdir [hyperparameter_file] [hyperparameter_number]\n

runtime_dir: path to MATLAB runtime library directory\n
mode: standalone, GLG, or Aggregate\n
Data: Path to single-cell expression data file\n
gene_list: File path to list of genes in the dataset\n
outdir: Directory path for storing temporary files and final ranked lists of gene interactions and influential genes\n
hyperparameter_file: file containing list of hyperparameter combinations for SINGE (required for standalone and GLG modes)\n
hyperparameter_number: 1-based hyperparameter index to use from the hyperparameter_file (required for GLG mode)"

if [[ $SINGE_RUNNING_IN_DOCKER ]]; then
	usage+="\n\nWhen running inside Docker with the default entry point, only the arguments after runtime_dir are required.
	The script name and runtime_dir argument are specified automatically."
fi

if [[ $# -eq 1 && $1 == "-h" ]]; then
	echo -e $usage
	exit 0
fi

# At least 5 arguments required in all modes
if [[ $# -lt 5 ]]; then
	echo Missing required arguments
	echo -e $usage
	exit 1
fi

# When SINGE is run inside Docker, the location of this script is needed
# in order to locate the compiled MATLAB executables and wrapper scripts
exe_dir=$(dirname "$0")

runtime=$1
mode=$2
data=$3
gene_list=$4
outdir=$5
hypefile=$6

shopt -s nocasematch

mode1=standalone
mode2=GLG
mode3=Aggregate
validMode=0

echo "SINGE operating in" $mode "mode"

# An optional suffix to add to the MATLAB-generated script filename
# to select the correct script and binaries for the OS
run_suffix=""
if [[ "$OSTYPE" == "darwin"* ]]; then
	echo "Using macOS SINGE binaries"
	run_suffix="_mac"
else
	echo "Using Linux SINGE binaries"
fi

if [[ $mode == $mode1 ]]; then 
	validMode=1
	echo $mode1 "mode running GLG tests"
	if [[ -z $hypefile ]]; then
		echo Missing hyperparameter_file argument
		echo -e $usage
		exit 1
	fi
	# Use grep instead of wc to be robust to a missing final newline
	nargs=$(grep -c "" $hypefile)
	for hypenum in $(seq 1 $nargs); do
	    echo hypenum: $hypenum
	    # Get the GLG arguments from the specified row in the hyperparameters file
	    arg=$(sed "$hypenum q;d" $hypefile)
	    echo arg: $arg
	    bash $exe_dir/run_SINGE_GLG_Test${run_suffix}.sh $runtime $data --outdir $outdir $arg
	done
elif [[ $mode == $mode2 ]]; then 
	validMode=1
	echo $mode2 "mode running"
	hypenum=$7
	if [[ -z $hypefile || -z $hypenum ]]; then
		echo Missing required arguments
		echo -e $usage
		exit 1
	fi
	echo hypenum: $hypenum
	# Get the GLG arguments from the specified row in the hyperparameters file
	arg=$(sed "$hypenum q;d" $hypefile)
	echo arg: $arg
	bash $exe_dir/run_SINGE_GLG_Test${run_suffix}.sh $runtime $data --outdir $outdir $arg
fi

if [[ $mode == $mode3 || $mode == $mode1 ]]; then 
	validMode=1
	echo $mode3 "mode running"
	bash $exe_dir/run_SINGE_Aggregate${run_suffix}.sh $runtime $data $gene_list $outdir
fi

if [[ $validMode == 0 ]]; then 
	echo Invalid SINGE mode. Please use one of the following modes: $mode1, $mode2, $mode3
	echo -e $usage
fi