install_dDocent_requirements

#!/bin/bash

###Script to check for and install most of the required software for dDocent

if [ -z "$1" ]; then
echo "Correct usage is sh install_dDocent_requirements [directory in your computer or user PATH]"
echo "if installing for all users, best to run this script as root"
exit 1
fi

INSTALL_PATH=$1

export PATH=$INSTALL_PATH:$PATH

echo "Checking for required software"

echo "Checking for cmake"
if which cmake &>/dev/null; then
    echo "cmake is already installed"
else
	echo "Downloading and installing cmake"
	curl -O https://cmake.org/files/v3.4/cmake-3.4.0-rc3.tar.gz
	tar xvzf cmake-3.4.0-rc3.tar.gz
	cd cmake-3.4.0-rc3
	./bootstrap --prefix=$INSTALL_PATH
	make
	make install
	ln -s $INSTALL_PATH/bin/* $INSTALL_PATH
	cd ..
fi

echo "Checking for FreeBayes"
if which freebayes &>/dev/null; then
    echo "FreeBayes is already installed"
else
        echo "Downloading and installing FreeBayes"
	git clone --recursive https://github.com/ekg/freebayes.git
	cd freebayes
        make
	cd bin
	chmod +x *
	cp -f * $INSTALL_PATH
	cd ..
	cd ./vcflib/
	make
	chmod +x ./bin/*
	cp -f ./bin/* $INSTALL_PATH
	cd ..
	cd ..
fi
echo "Checking for vcflib"
if which vcfcombine &>/dev/null; then
    echo "vcflib is already installed"
else
        echo "Downloading and installing vcflib"
	git clone --recursive git://github.com/ekg/freebayes.git
        cd freebayes
	cd ./vcflib/
	make
	chmod +x ./bin/*
	cp -f ./bin/* $INSTALL_PATH
	cd ..
	cd ..
fi

echo "Checking for Trimmomatic"

if find ${PATH//:/ } -maxdepth 1 -name trimmomatic*jar 2> /dev/null | awk '/./' ; then
    echo "Trimmomatic is already installed"
else
	echo "Downloading and installing Trimmomatic"
	curl -O http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip
	unzip Trimmomatic-0.33.zip
	cd Trimmomatic-0.33
	cp -f ./adapters/* $INSTALL_PATH
	cp -f trimmomatic-0.33.jar $INSTALL_PATH
	cd ..
fi

if find ${PATH//:/ } -maxdepth 1 -name TruSeq2-PE.fa 2> /dev/null | grep -q '.' ; then
     echo "Trimmomatic adapters already installed"
else
    	echo "Downloading and installing Trimmomatic"
        curl -O http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip
        unzip Trimmomatic-0.33.zip
        cd Trimmomatic-0.33
        cp -f ./adapters/* $INSTALL_PATH
        cp -f trimmomatic-0.33.jar $INSTALL_PATH
	cd ..
fi


echo "Checking for mawk"
if which mawk &>/dev/null; then
    echo "mawk is already installed"
else
	echo "Downloading and installing mawk"
	curl -O http://invisible-island.net/datafiles/release/mawk.tar.gz
	tar xvzf mawk.tar.gz
	cd mawk-1.*
	./configure
	make
	chmod +x mawk
	cp -f mawk $INSTALL_PATH
	cd ..
fi

echo "Checking for bwa"
if which bwa &>/dev/null; then
    echo "bwa is already installed"
else
    echo "Downloading and installing bwa"
	git clone https://github.com/lh3/bwa.git
	cd bwa
	make
	chmod +x bwa
	cp -f bwa $INSTALL_PATH
	cd ..
fi

echo "Checking for samtools"
if which samtools &>/dev/null; then
    echo "samtools is already installed"
else
	echo "Downloading and installing samtools"
	curl -L -o samtools-1.3.1.tar.bz2 "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
	tar xvjf samtools-1.3.1.tar.bz2 
	cd samtools-1.3.1/
	./configure
	make
	chmod +x samtools
	cp -f samtools $INSTALL_PATH
	cd ..
fi

echo "Checking for VCFtools"
if which vcftools &>/dev/null; then
    echo "VCFtools is already installed"
else
	echo "Downloading and installing VCFtools"
	curl -L -o vcftools_x.tar.gz "https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz"	
	tar xvzf vcftools_x.tar.gz
	cd vcftools-*
	./configure
	make
	chmod +x ./src/cpp/vcftools
	cp -f ./src/cpp/vcftools $INSTALL_PATH
	cd ..
fi

echo "Checking for Rainbow"
if which rainbow &>/dev/null; then
        VER=(`rainbow | head -1 | cut -f2 -d' ' `)	
	if [[ "$VER" == "2.0.2" || "$VER" == "2.0.3" || "$VER" == "2.0.4" ]]; then
        	echo "Rainbow is already installed"
	else
		echo "Downloading and installing Rainbow"
        	curl -L -o rainbow.x.tar.gz "http://sourceforge.net/projects/bio-rainbow/files/latest/download?source=files"
        	tar xvzf rainbow.x.tar.gz
        	cd rainbow_*
        	make
        	chmod +x rainbow rbasm rbmergetag select_*
        	cp -f rainbow rbasm rbmergetag select_* $INSTALL_PATH
		cd ..
	fi
else
	echo "Downloading and installing Rainbow"
	curl -L -o rainbow.x.tar.gz "http://sourceforge.net/projects/bio-rainbow/files/latest/download?source=files"
	tar xvzf rainbow.x.tar.gz
	cd rainbow_*
	make
	chmod +x rainbow rbasm rbmergetag select_*
	cp -f rainbow rbasm rbmergetag select_* $INSTALL_PATH	
	cd ..
fi

echo "Checking for gnuplot"
if which gnuplot &>/dev/null; then
	echo "gnuplot is already installed"
else
	echo "Downliading and installing gnuplot"
	curl -L -o gnuplot.x.tar.gz "http://sourceforge.net/projects/gnuplot/files/latest/download?source=files"
	tar xvzf gnuplot.x.tar.gz 
	cd gnuplot-* 
	current=`pwd` 
	./configure --prefix=$current/gnuplot_install 
	make install
	chmod +x gnuplot_install/bin/gnuplot
	cp -f gnuplot_install/bin/gnuplot $INSTALL_PATH 
	cd .. 
fi

echo "Checking for seqtk"
if which seqtk &>/dev/null; then
    echo "seqtk is already installed"
else
    	echo "Downloading and installing seqtk"
	git clone https://github.com/lh3/seqtk.git
	cd seqtk
	make
	chmod +x seqtk
	cp -f seqtk $INSTALL_PATH	
	cd ..
fi

echo "Checking for cd-hit"
if which cd-hit-est &>/dev/null; then
    echo "cd-hit is already installed"
else
	echo "Downloading and installing cd-hit"
	curl -L -O https://github.com/weizhongli/cdhit/releases/download/V4.6.6/cd-hit-v4.6.6-2016-0711.tar.gz
	tar xvzf cd-hit-v4.6.6-2016-0711.tar.gz
	cd cd-hit-v4.6.6-2016-0711
	make openmp=yes
	chmod +x cd-hit-est cd-hit-est-2d
	cp -f cd-hit-est cd-hit-est-2d $INSTALL_PATH
	cd ..
fi

echo "Checking for bedtools"
if which bamToBed &>/dev/null; then
    	echo "bedtools is already installed"
else
	curl -L -O https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz
	tar xvzf bedtools-2.26.0.tar.gz 
	cd bedtools2
	make 
	cd bin
	chmod +x *
	cp -f * $INSTALL_PATH
	cd ..
	cd ..
fi

echo "Checking for bedops"
if which bedops &>/dev/null; then
	echo "bedops is already installed"
else
	git clone https://github.com/bedops/bedops.git
	cd bedops
	make all
	make install
	cp -f bin/* $INSTALL_PATH
	cd ..
fi

echo "Checking for bamtools"
if which bamtools &>/dev/null; then
	echo "bamtools is already installed"
else
	git clone https://github.com/pezmaster31/bamtools.git
	cd bamtools
	mkdir build
	cd build
	cmake ..
	make
	cd ../bin
	chmod +x bamtools
	cp -f bamtools $INSTALL_PATH
	cd ..
	cd ..
fi

echo "Checking for GNU-parallel"
if which parallel &>/dev/null; then
    	echo "GNU-parallel is already installed"
else
	curl -L -O http://ftp.gnu.org/gnu/parallel/parallel-latest.tar.bz2
	tar xvjf parallel-latest.tar.bz2
	rm parallel-latest.tar.bz2
	cd parallel*
	./configure && make
	chmod +x ./src/parallel ./src/sem ./src/niceload ./src/sql
	cp -f ./src/parallel ./src/sem ./src/niceload ./src/sql $INSTALL_PATH
	cd ..
fi

echo "Checking for PEAR (read merger)"
if which pearRM &>/dev/null; then
	echo "pear is already installed"
else
	curl -L -O http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.6-bin-64.tar.gz
	tar vxzf pear-0.9.6-bin-64.tar.gz 
	cd pear-0.9.6-bin-64
	cp -f pear-0.9.6-bin-64 pearRM
	chmod +x pearRM
	cp -f pearRM $INSTALL_PATH
	cd ..
fi	
	
echo "Now installing dDocent"
	curl -L -O https://github.com/jpuritz/dDocent/raw/master/dDocent
	chmod +x dDocent
	cp -f dDocent $INSTALL_PATH