install.sh

#!/bin/bash

usage()
{
	USAGE="""
MToolBox: a tool for heteroplasmy annotation and accurate functional analysis of mitochondrial variants from high throughput sequencing data.
Written by Domenico Simone, Claudia Calabrese and Maria Angela Diroma 2013-2014.
	
Usage:

FOR FULL INSTALLATION (strongly recommended):
./install.sh

FOR FULL INSTALLATION ON OSX:
./install.sh -o

TO CHANGE SOME OF THE SOFTWARE VERSIONS/KMER PARAMETER DURING THE FULL INSTALLATION OF MTOOLBOX:
./install.sh -g <gsnap_version> -z <zlib_version> -m <muscle_file> -s <samtools_version> -k <kmer_to_build_gsnap_db>

TO UPDATE ONLY ONE SPECIFIC SOTWARE:
./install.sh -i <software_name>

followed, in case, by one of the options to specify the software version/kmer parameter:
	-g	GSNAP version: default is 2015-12-31.v7
	-a	Anaconda version: default is 2-2.5.0
	-z	Zlib version: default is 1.2.11
	-m 	MUSCLE version: default is muscle3.8.31_i86linux64
	-s 	Samtools version: default is 1.3
	-k	Kmer used for GSNAP database: default is 15
	-i	install only one specific software [gsnap | anaconda | muscle | zlib | samtools | gsnap_db]

Help options:

	-h	show this help message
	"""
	echo "$USAGE"
}

gsnap_gmap_version=2015-12-31.v7
anaconda_version=2-2.5.0
anaconda_file=Anaconda$anaconda_version-Linux-x86_64.sh
muscle_file=muscle3.8.31_i86linux64
samtools_version=1.3
zlib_version=1.2.11
kmer=15
opsys=linux
software_install=all

while getopts ":hg:s:m:a:z:k:i:o" opt; do
	case $opt in
		h)
			usage
			exit 1
			;;
		g)
			gsnap_gmap_version=$OPTARG
			;;
		s)
			samtools_version=$OPTARG
			;;
		m)
			muscle_file=$OPTARG
			;;
		a)
			anaconda_version=$OPTARG
			;;
		z)
			zlib_version=$OPTARG
			;;
		k)
			kmer=$OPTARG
			;;
		i)
			software_install=$OPTARG
			;;
		o)
		    muscle_file=muscle3.8.31_i86darwin64
		    anaconda_file=Anaconda$anaconda_version-MacOSX-x86_64.sh
		    opsys=osx
		    ;;
		\?)
			echo "Invalid option: -$OPTARG" >&2
			exit 1
			;;
		:)
			echo "Option -$OPTARG requires an argument." >&2
			exit 1
			;;
	esac
done

download()
{
    URL=$1
    OFILE=$2
    wget  --no-check-certificate -c -nc -L "$URL" -O $OFILE
}

muscle_install()
{
	echo "Installing Muscle $muscle_file ..."
	muscle_file=$muscle_file
	muscle_url=http://www.drive5.com/muscle/downloads3.8.31/${muscle_file}.tar.gz
	pushd .
	cd bin
	if [ "$opsys" == "osx" ]; then
	    curl -k $muscle_url -o $muscle_file.tar.gz
    else
    	download $muscle_url $muscle_file.tar.gz
    fi
	tar -zxvf $muscle_file.tar.gz
	popd
	echo "Installing Muscle $muscle_file... Done."
}

samtools_install()
{
	echo "Installing Samtools $samtools_version"
	samtools_version=$samtools_version
	samtools_file=samtools-${samtools_version}.tar.bz2
	#samtools_url=https://github.com/samtools/samtools/releases/download/1.3/$samtools_file
	samtools_url=https://kent.dl.sourceforge.net/project/samtools/samtools/1.3/$samtools_file
	pushd .
	cd bin
	if [ "$opsys" == "osx" ]; then
	    curl -k $samtools_url -o $samtools_file
    else
    	download $samtools_url $samtools_file
    fi
	tar xjvf $samtools_file
	cd samtools-${samtools_version}
	./configure
	make
	make prefix=../samtools/ install
	popd
	echo "Installing Samtools $samtools_file... Done."
}

zlib_install() {
	echo "Installing zlib $zlib_version ..."
	zlib_version=$zlib_version
	zlib_file=zlib-${zlib_version}.tar.gz
	zlib_url=http://zlib.net/$zlib_file
	pushd .
	cd bin
	if [ "$opsys" == "osx" ]; then
	    curl -k $zlib_url -o $zlib_file
    else
    	download $zlib_url $zlib_file
    fi
	tar xvzf $zlib_file
	cd zlib-${zlib_version}
	./configure --prefix ../zlib
	make
	make install
	popd
	echo  "Installing zlib $zlib_version... Done."
	echo "Exporting zlib..."
	export LD_LIBRARY_PATH=$MTOOLBOX_BIN/zlib/lib:$LD_LIBRARY_PATH:/usr/local/lib
	export CFLAGS="-I$MTOOLBOX_BIN/zlib/include $CFLAGS"
}

gsnap_install() {
	echo "Installing gmap $gsnap_gmap_version..."
	gsnap_gmap_file=gmap-gsnap-${gsnap_gmap_version}.tar.gz
	gsnap_gmap_url=http://research-pub.gene.com/gmap/src/$gsnap_gmap_file
	pushd .
	cd bin
	if [ "$opsys" == "osx" ]; then
	    curl -k $gsnap_gmap_url -o $gsnap_gmap_file
    else
    	download $gsnap_gmap_url $gsnap_gmap_file
    fi
	tar xvzf $gsnap_gmap_file &&
	rm $gsnap_gmap_file
	cd gmap*
	./configure --prefix=$MTOOLBOX_BIN/gmap
	make
	make install
	echo "Installing gmap $gsnap_gmap_version... Done."
	popd
}

gsnap_db_install() {
	nfasta_rcrs_url=http://sourceforge.net/projects/mtoolbox/files/genome_fasta/hg19RCRS.fa.gz
	nfasta_rcrs=hg19RCRS.fa.gz
	nfasta_rsrs_url=http://sourceforge.net/projects/mtoolbox/files/genome_fasta/hg19RSRS.fa.gz
	nfasta_rsrs=hg19RSRS.fa.gz
	rcrs_mfasta_url=http://sourceforge.net/projects/mtoolbox/files/genome_fasta/chrM.fa.gz
	rcrs_mfasta=chrM.fa.gz
	rsrs_mfasta_url=http://sourceforge.net/projects/mtoolbox/files/genome_fasta/chrRSRS.fa.gz
	rsrs_mfasta=chrRSRS.fa.gz
	if [ "$opsys" == "osx" ]; then
	    curl -L $nfasta_rcrs_url -o $nfasta_rcrs
	    curl -L $nfasta_rsrs_url -o $nfasta_rsrs
	    curl -L $rcrs_mfasta_url -o $rcrs_mfasta
	    curl -L $rsrs_mfasta_url -o $rsrs_mfasta
    else
    	download $nfasta_rcrs_url $nfasta_rcrs
	    download $nfasta_rsrs_url $nfasta_rsrs
	    download $rcrs_mfasta_url $rcrs_mfasta
	    download $rsrs_mfasta_url $rsrs_mfasta
    fi

	if [ "$decompress_fasta" == True ]; then
		echo "Building gmap db using $nfasta_rcrs..."
		$MTOOLBOX_BIN/gmap/bin/gmap_build -D $gmap_db -d $database_name_nfasta_rcrs -g $nfasta_rcrs -s numeric-alpha -k $kmer
		echo "Building gmap db using $nfasta_rsrs..."
		$MTOOLBOX_BIN/gmap/bin/gmap_build -D $gmap_db -d $database_name_nfasta_rsrs -g $nfasta_rsrs -s numeric-alpha -k $kmer
		echo "Building gmap db using $rcrs_mfasta..."
		$MTOOLBOX_BIN/gmap/bin/gmap_build -D $gmap_db -d $database_name_rcrs -g $rcrs_mfasta -s numeric-alpha -k $kmer
		echo "Building gmap db using $rsrs_mfasta..."
		$MTOOLBOX_BIN/gmap/bin/gmap_build -D $gmap_db -d $database_name_rsrs -g $rsrs_mfasta -s numeric-alpha -k $kmer
	else
        echo "Building gmap db using $nfasta_rcrs..."
        $MTOOLBOX_BIN/gmap/bin/gmap_build -D $gmap_db -d $database_name_nfasta_rcrs $nfasta_rcrs -s numeric-alpha -k $kmer
        echo "Building gmap db using $nfasta_rsrs..."
        $MTOOLBOX_BIN/gmap/bin/gmap_build -D $gmap_db -d $database_name_nfasta_rsrs $nfasta_rsrs -s numeric-alpha -k $kmer
        echo "Building gmap db using $rcrs_mfasta..."
        $MTOOLBOX_BIN/gmap/bin/gmap_build -D $gmap_db -d $database_name_rcrs $rcrs_mfasta -s numeric-alpha -k $kmer
        echo "Building gmap db using $rsrs_mfasta..."
        $MTOOLBOX_BIN/gmap/bin/gmap_build -D $gmap_db -d $database_name_rsrs $rsrs_mfasta -s numeric-alpha -k $kmer
	fi
	echo "Building gmap db... Done."
}

anaconda_install() {
	echo "Installing Anaconda version $anaconda_version..."
	anaconda_file=Anaconda$anaconda_version-Linux-x86_64.sh
	#anaconda_file=$anaconda_file
	unset PYTHONPATH
	if [ "$opsys" == "osx" ]; then
	    curl -k https://repo.anaconda.com/archive/$anaconda_file -o $anaconda_file
    else
	echo $anaconda_file
	download https://repo.anaconda.com/archive/${anaconda_file} $anaconda_file
    fi
	chmod +x $anaconda_file
	mkdir -p $MTOOLBOX_BIN/anaconda
	./$anaconda_file -p $MTOOLBOX_BIN/anaconda -b -f
	echo "Installing Anaconda... Done."
	echo "Exporting Anaconda path: $MTOOLBOX_BIN/anaconda/bin"
	export PATH=$MTOOLBOX_BIN/anaconda/bin:$PATH
}

#########################################
decompress_fasta=True
database_name_rcrs=chrM
database_name_rsrs=chrRSRS
database_name_nfasta_rcrs=hg19RCRS
database_name_nfasta_rsrs=hg19RSRS
DIRECTORY=bin
if [ -d "$DIRECTORY" ]; then
	echo "$DIRECTORY already exists..."
else
	echo "Creating $DIRECTORY..."
	mkdir $DIRECTORY
fi

if [ "$opsys" == "osx" ]; then
    MTOOLBOX_BIN=`pwd`/$DIRECTORY
else
    MTOOLBOX_BIN=$(readlink -f $DIRECTORY)
fi

GENOME_FASTA=genome_fasta
if [ -d "$GENOME_FASTA" ]; then
        echo "$GENOME_FASTA already exists..."
else
        echo "Creating $GENOME_FASTA..."
        mkdir $GENOME_FASTA
fi

gmap_db=gmapdb
if [ -d "$gmap_db" ]; then
        echo "$gmap_db already exists..."
else
        echo "Creating $gmap_db..."
        mkdir $gmap_db
fi

MTOOLBOX_DIR=$(pwd)

if [ "$software_install" == 'all' ]; then
	echo "Installing anaconda, zlib, samtools, muscle, gsnap, gsnap_db..."

    anaconda_install
	zlib_install
	#echo "exporting zlib to generate gmap db..."
	#export LD_LIBRARY_PATH=$MTOOLBOX_BIN/zlib/lib:$LD_LIBRARY_PATH:/usr/local/lib
	#export CFLAGS="-I$MTOOLBOX_BIN/zlib/include $CFLAGS"
	samtools_install
	muscle_install
	gsnap_install
	gsnap_db_install

	echo "Moving fasta files into $GENOME_FASTA..."

	mv $rcrs_mfasta $GENOME_FASTA
	mv $rsrs_mfasta $GENOME_FASTA
	mv $nfasta_rcrs $GENOME_FASTA
	mv $nfasta_rsrs $GENOME_FASTA

	if [ "$decompress_fasta"==True ]; then
		cd $GENOME_FASTA
		echo "Decompressing nfasta..."
		for i in $(ls *.gz); do gzip -d $i; done &&
		cd ..
		echo "Done."
	else
		echo "Done."
	fi

	echo "Generating fasta.fai indexes with samtools..."
	cd $GENOME_FASTA
	ls * > fasta.lst
	for i in $(cat fasta.lst); do
	    $MTOOLBOX_BIN/samtools/bin/samtools faidx $i;
    done
	echo "Installation completed."
	cd ..
else
	echo "Installing $software_install..."
	${software_install}_install
	echo "Installation completed."
fi

SETUP_FILE=${MTOOLBOX_DIR}/MToolBox/setup.sh

cat <<EOF > $SETUP_FILE
#! /bin/bash

export MTOOLBOX_DIR=$MTOOLBOX_DIR
export MTOOLBOX_BIN=$MTOOLBOX_BIN
export PATH=\$MTOOLBOX_BIN/anaconda/bin:\$PATH
export PYTHONUSERBASE=\$MTOOLBOX_BIN/anaconda
export LD_LIBRARY_PATH=\$MTOOLBOX_BIN/zlib/lib:\$LD_LIBRARY_PATH:/usr/local/lib
export CFLAGS="-I\$MTOOLBOX_BIN/zlib/include \$CFLAGS"
export samtoolsexe=\$MTOOLBOX_BIN/samtools-${samtools_version}/samtools
export muscleexe=\$MTOOLBOX_BIN/$muscle_file
export gsnapexe=\$MTOOLBOX_BIN/gmap/bin/gsnap
fasta_path=\$MTOOLBOX_DIR/$GENOME_FASTA/
gsnapdb=\$MTOOLBOX_DIR/$gmap_db/
samtools_version=$samtools_version
mtdb_fasta=chrRSRS.fa
hg19_fasta=hg19RSRS.fa
mtdb=chrRSRS
humandb=hg19RSRS
EOF

exit 0