NeoFuse

#! /bin/bash

realpath2 ()
{
    relpath=$1
    cpath=`pwd`
    reldir=`dirname $relpath`
    relfile=`basename $relpath`
    cd $reldir
    abspath=`pwd`
    abspath=$abspath"/"$relfile
    cd $cpath
    echo $abspath
}

OUTDIR="./"
declare -i PEPMAX
declare -i PEPMIN
PEPMIN=8
declare -i CORES
CORES=1
declare -i RAMLIMIT
RAMLIMIT=0
THRESHOLD=""
RANK=""
CONF="L"
NETMHCPAN="false"
BUILD="false"
BUILDREF="false"
VERSION="GRCh38"

while getopts ":1::2::d::i::o::m::M::n::t::T::c::s::g::a::l::-::N::BRV::h" opt;
do
	case $opt in
	1)	READ1="$OPTARG";;
	2)	READ2="$OPTARG";;
	d)	ID="$OPTARG";;
	i)	IN="$OPTARG";;
	o)  OUTDIR="$OPTARG";;
	m)	PEPMIN="$OPTARG";;
	M)	PEPMAX="$OPTARG";;
	n)	CORES="$OPTARG";;
	t)	THRESHOLD="$OPTARG";;
	T)	RANK="$OPTARG";;
	c)	CONF="$OPTARG";;
	s)	STARINDEX="$OPTARG";;
	g)	GENOMEDIR="$OPTARG";;
	a)	ANNOTATION="$OPTARG";;
	N)	NETMHCPAN="$OPTARG";;
	l)	RAMLIMIT="$OPTARG";;
	-)	IMAGE="$OPTARG";;
	B)	BUILD="true";;
	R)	BUILDREF="true";;
	V)	VERSION="$OPTARG";;
	h)	HELP="true";;
	esac
done
if [ "$BUILD" == "false" ]; then
	if [ "$READ1" == "" ] && [ "$IN" == "" ] && [ "$BUILDREF" == "false" ] || [ "$HELP" == "true" ]; then
		echo "Usage: NeoFuse <arguments> [options]

	<Arguments>

	-1: Path to read 1 FASTQ file (mandatory only for single sample analysis)
	-2: Path to read 2 FASTQ fie (optional for single-end reads)
	-i: Path to TSV file (mandatory only for multiple sample analysis)
	-s: Path to STAR index directory
	-g: Path to reference genome FASTA file 
	-a: Path to annotation GTF file
	-o: Output directory (default: "./")
	-d: Run ID (default: input filename)

	-B: Build singularity/docker image
	-R: Build indexes

	[Options]

	-m: Minimum peptide length (8, 9, 10, or 11; default: 8)
	-M: Maximum peptide length (8, 9, 10, or 11; default: 8)
	-n: Number of cores (default: 1)
	-t: IC50 binding affinity threshold (default: 500)
	-T: Percentile rank threshold (default: Inf)
	-c: Mimimum confidence score (H, M or L; default: L)

	--singularity: NeoFuse will use the Singularity image
	--docker: NeoFuse will use the Docker image
	
	For more information please refer to https://icbi.i-med.ac.at/software/NeoFuse/
	"
		exit 0
	else
		:
	fi
	if [ "$BUILDREF" == "true" ]; then
		SOURCE="${BASH_SOURCE[0]}"
		while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
		DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
		SOURCE="$(readlink "$SOURCE")"
		[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE is a relative symlink, resolve it relative to the path where the symlink file is located
		done
		DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
		OUTDIR=`realpath2 $OUTDIR`
		mkdir -p $OUTDIR
		if [ "$IMAGE" == "docker" ]; then
			DMOUNT="-v $OUTDIR:/mnt/out/$(echo ${OUTDIR##*/})"
			OUTDIR="/mnt/out/$(echo ${OUTDIR##*/})"
			docker run $DMOUNT icbi/neofuse NeoFuse-download -o $OUTDIR -t $CORES -v $VERSION
			exit 0
		elif [ "$IMAGE" == "singularity" ]; then
			SMOUNT="-B $OUTDIR:/mnt/out/$(echo ${OUTDIR##*/})"
			OUTDIR="/mnt/out/$(echo ${OUTDIR##*/})"
			singularity exec $SMOUNT $DIR"/NeoFuse.sif" NeoFuse-download -o $OUTDIR -t $CORES -v $VERSION
			exit 0
		else
			echo "You must specify '--docker' or '--singularity'"
			echo "Exiting ..."
			exit 1
		fi
	else
		:
	fi
	if [ "$THRESHOLD" == "" ] && [ "$RANK" == "" ]; then
		THRESHOLD=500
		RANK=inf
	elif [ "$THRESHOLD" != "" ] && [ "$RANK" == "" ]; then
		RANK=inf
	elif [ "$THRESHOLD" == "" ] && [ "$RANK" != "" ]; then
		THRESHOLD=inf
	fi
	if [ "$NETMHCPAN" == "false" ]; then
		:
	else
		NETMHCPAN=`realpath2 $NETMHCPAN`
		if [ ! -d "$NETMHCPAN" ]; then
			echo "No local netMHCpan instalation found"
			echo "Install netMHCpan and try again"
			echo "Exiting ..."
			exit 1
		else
			:
		fi
	fi

	if test $ID; then
		:
	else
		ID=$(echo ${READ1##*/} | sed s/_.*fastq.*//)
	fi

	if [ "$PEPMAX" == "" ]; then
		PEPMAX=$PEPMIN
	fi

	if [ "$IN" != "" ] && [ "$READ1" != "" ]; then
		echo " You may specify as input a TSV file OR FASTQ file(s), but not both "
		echo "Exiting ..."
		exit 1
	fi

	if [ "$IN" != "" ] && [ "$READ2" != "" ]; then
		echo " You may specify as input a TSV file OR FASTQ file(s), but not both "
		echo "Exiting ..."
		exit 1
	fi

	if [ "$STARINDEX" == "" ]; then
		echo "You must specify a STAR index directory"
		echo "Exiting ..."
		exit 1
	elif [ "$GENOMEDIR" == "" ]; then
		echo "You must specify a FASTA reference file"
		echo "Exiting ..."
		exit 1
	elif [ "$ANNOTATION" == "" ]; then
		echo "You must specify an annotation GTF file"
		echo "Exiting ..."
		exit 1
	fi

	# Convert relative to absolute paths
	if [ "$IN" != "" ]; then
		IN=`realpath2 $IN`
	fi

	if [ "$READ1" != "" ]; then
		READ1=`realpath2 $READ1`
	fi

	if [ "$READ2" != "" ]; then
		READ2=`realpath2 $READ2`
	fi

	mkdir -p $OUTDIR
	OUTDIR=`realpath2 $OUTDIR`
	STARINDEX=`realpath2 $STARINDEX`
	GENOMEDIR=`realpath2 $GENOMEDIR`
	ANNOTATION=`realpath2 $ANNOTATION`

	# Get the source dir
	SOURCE="${BASH_SOURCE[0]}"
	while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
		DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
		SOURCE="$(readlink "$SOURCE")"
		[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE is a relative symlink, resolve it relative to the path where the symlink file is located
	done
	DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
	
	if [ "$IMAGE" == "docker" ] || [ "$IMAGE" == "singularity" ] || [ "$IMAGE" == "" ]; then
		:
	else
		echo "Invalid parameter, accepted values are: [--singularity], [--docker], []"
		echo "Exiting ..."
		exit 1
	fi

	if [ "$IMAGE" == "docker" ] || [ "$IMAGE" == "singularity" ] ; then
		# If user calls for Docker/singularity:
		## Change realpaths to mount points
		if [ "$IN" != "" ]; then
			cat $IN > $(echo $IN | sed s/.tsv//)_temp.tsv
			IN=$(echo $IN | sed s/.tsv//)_temp.tsv
			INDIR=$(awk '{if(NR==2){ print $2; }}' < "$IN")
			INDIR=$(dirname "${INDIR}")
			sed -i "s%$INDIR%/mnt/data%g" $IN
			INDIR=`realpath2 $INDIR`
			SMOUNT="-B $INDIR:/mnt/data,$IN:/mnt/$(echo ${IN##*/}),$OUTDIR:/mnt/out/$(echo ${OUTDIR##*/}),$STARINDEX:/mnt/genome/$(echo ${STARINDEX##*/}),$GENOMEDIR:/mnt/genome/$(echo ${GENOMEDIR##*/}),$ANNOTATION:/mnt/genome/$(echo ${ANNOTATION##*/})"
			DMOUNT="-v $INDIR:/mnt/data -v $IN:/mnt/$(echo ${IN##*/}) -v $OUTDIR:/mnt/out/$(echo ${OUTDIR##*/}) -v $STARINDEX:/mnt/genome/$(echo ${STARINDEX##*/}) -v $GENOMEDIR:/mnt/genome/$(echo ${GENOMEDIR##*/}) -v $ANNOTATION:/mnt/genome/$(echo ${ANNOTATION##*/})"
			if [ "$NETMHCPAN" == "false" ]; then
				:
			else
				SMOUNT=$SMOUNT",$NETMHCPAN:/usr/local/bin/source/$(echo ${NETMHCPAN##*/})"
				DMOUNT=$DMOUNT" -v $NETMHCPAN:/usr/local/bin/source/$(echo ${NETMHCPAN##*/})"
			fi
			IN="/mnt/$(echo ${IN##*/})"
		fi

		if [ "$READ1" != "" ]; then
			SMOUNT="-B $READ1:/mnt/data/$(echo ${READ1##*/}),$OUTDIR:/mnt/out/$(echo ${OUTDIR##*/}),$STARINDEX:/mnt/genome/$(echo ${STARINDEX##*/}),$GENOMEDIR:/mnt/genome/$(echo ${GENOMEDIR##*/}),$ANNOTATION:/mnt/genome/$(echo ${ANNOTATION##*/})"
			DMOUNT="-v $READ1:/mnt/data/$(echo ${READ1##*/}) -v $OUTDIR:/mnt/out/$(echo ${OUTDIR##*/}) -v $STARINDEX:/mnt/genome/$(echo ${STARINDEX##*/}) -v $GENOMEDIR:/mnt/genome/$(echo ${GENOMEDIR##*/}) -v $ANNOTATION:/mnt/genome/$(echo ${ANNOTATION##*/})"
			if [ "$NETMHCPAN" == "false" ]; then
				:	
			else
				SMOUNT=$SMOUNT",$NETMHCPAN:/usr/local/bin/source/$(echo ${NETMHCPAN##*/})"
				DMOUNT=$DMOUNT" -v $NETMHCPAN:/usr/local/bin/source/$(echo ${NETMHCPAN##*/})"
			fi
		fi

		if [ "$READ2" != "" ]; then
			SMOUNT=$SMOUNT",$READ2:/mnt/data/$(echo ${READ2##*/})"
			DMOUNT=$DMOUNT" -v $READ2:/mnt/data/$(echo ${READ2##*/})"
			READ2="/mnt/data/$(echo ${READ2##*/})"	
		fi
		mkdir -p $OUTDIR
		REALOUT=$OUTDIR
		OUTDIR="/mnt/out/$(echo ${OUTDIR##*/})"
		STARINDEX="/mnt/genome/$(echo ${STARINDEX##*/})"
		GENOMEDIR="/mnt/genome/$(echo ${GENOMEDIR##*/})"
		ANNOTATION="/mnt/genome/$(echo ${ANNOTATION##*/})"
		READ1="/mnt/data/$(echo ${READ1##*/})"
		if [ "$NETMHCPAN" == "false" ]; then
			:
		else
			NETMHCPAN="/usr/local/bin/source/$(echo ${NETMHCPAN##*/})"
		fi

		## Check for Docker/singularity installation and launch
		if [ "$IMAGE" == "docker" ]; then
			if [ -x "$(command -v docker)" ]; then
				if [ "$IN" != "" ]; then
					docker run -rm $DMOUNT icbi/neofuse NeoFuse_multi -i $IN -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT
				elif [ "$READ1" != "" ]; then
					if [ "$READ2" == "" ]; then
						docker run -rm $DMOUNT icbi/neofuse NeoFuse_single -1 $READ1 -d $ID -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT
					else
						docker run -rm $DMOUNT icbi/neofuse NeoFuse_single -1 $READ1 -2 $READ2 -d $ID -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT
					fi
				else
					echo "Invalid arguments"
					echo "Please check your input files"
					echo "Exiting ..."
					rm $IN
					exit 1
				fi
			else
				echo "No Docker instalation found on the machine"
				echo "Install Docker and try again"
				echo "Exiting ..."
				rm $IN
				exit 1
			fi
		elif [ "$IMAGE" == "singularity" ]; then
			if [ -x "$(command -v singularity)" ]; then
				if [ ! -e $DIR/NeoFuse.sif ]; then
					echo "No NeoFuse singularity image found locally"
					echo 'Try running: $ NeoFuse -B --singularity'
					exit 1
				fi
				if [ "$IN" != "" ]; then
					singularity exec $SMOUNT $DIR"/NeoFuse.sif" NeoFuse_multi -i $IN -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT
				elif [ "$READ1" != "" ]; then
					if [ "$READ2" == "" ]; then
						singularity exec $SMOUNT $DIR"/NeoFuse.sif" NeoFuse_single -1 $READ1 -d $ID -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT
					else
						singularity exec $SMOUNT $DIR"/NeoFuse.sif" NeoFuse_single -1 $READ1 -2 $READ2 -d $ID -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -T $RANK -t $THRESHOLD -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN -l $RAMLIMIT -r $REALOUT
					fi
				else
					echo "Invalid arguments"
					echo "Please check your input files"
					echo "Exiting ..."
					rm $IN
					exit 1
				fi
			else
				echo "No singularity instalation found on the machine"
				echo "Install singularity and try again"
				echo "Exiting ..."
				rm $IN
				exit 1
			fi
		elif [ "$IMAGE" == "" ]; then
			:
		else
			echo "Invalid paramater: accepted arguments are --docker or --singularity"
			echo "Exiting ..."
			rm $IN
			exit 1
		fi
	else
		# Check for multiple or single sample(s) - call the appropriate script
		# if [ "$IN" != "" ]; then
		# 	bash $DIR"/source/"NeoFuse_multi.sh -i $IN -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN
		# elif [ "$READ1" != "" ]; then
		# 	bash $DIR"/source/"NeoFuse_single.sh -1 $READ1 -2 $READ2 -d $ID -o $OUTDIR -m $PEPMIN -M $PEPMAX -n $CORES -t $THRESHOLD -T $RANK -c $CONF -s $STARINDEX -g $GENOMEDIR -a $ANNOTATION -N $NETMHCPAN
		# else
		# 	echo "Invalid arguments"
		# 	echo "Please check your input files"
		# 	echo "Exiting ..."
		# 	exit 1
		# fi
		echo "Missing argument: '--docker' or '--singularity'"
		echo "Exiting ..."
		exit 1
	fi
elif [ "$BUILD" == "true" ]; then
	# Get the source dir
	SOURCE="${BASH_SOURCE[0]}"
	while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
		DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
		SOURCE="$(readlink "$SOURCE")"
		[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE is a relative symlink, resolve it relative to the path where the symlink file is located
	done
	DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
	
	if [ "$IMAGE" == "docker" ]; then
		echo "Pulling NeoFuse Docker image from icbi repository"
		docker pull icbi/neofuse
	elif [ "$IMAGE" == "singularity" ]; then
		echo "Building NeoFuse Singularity image"
		singularity build $DIR"/NeoFuse.sif" docker://icbi/neofuse
	else
		echo "You must specify '--docker' or '--singularity'"
		echo "Exiting ..."
		exit 1
	fi
fi