install-dependencies.sh

#!/bin/bash
set -e

# install the following libraries using bash in linux
# boost, eigen, gsl, jellyfish, htslib, spline

Dir=$(pwd)

mkdir -p ${Dir}/external

# check pkg-config path
mkdir -p ${Dir}/external/pkgconfig
export PKG_CONFIG_PATH="${Dir}/external/pkgconfig/:${PKG_CONFIG_PATH}"

# install boost
echo "Install Boost library..."
cd ${Dir}/external
wget https://dl.bintray.com/boostorg/release/1.69.0/source/boost_1_69_0.tar.gz
tar -zxf boost_1_69_0.tar.gz
cd ${Dir}/external/boost_1_69_0
mkdir -p Installation
./bootstrap.sh --with-libraries=iostreams --prefix=${Dir}/external/boost_1_69_0/Installation
./b2 install 


# install eigen
if $(pkg-config --exists eigen3); then
	echo "EIGEN library exists."
else
	echo "Install Eigen library..."
	cd ${Dir}/external
	wget -O eigen-3.3.7.tar.gz http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
        mkdir -p eigen-3.3.7
	tar -xzf 3.3.7.tar.gz -C eigen-3.3.7 --strip-components=1
	cd eigen-3.3.7
	mkdir -p Installation
	mkdir -p build_dir && cd build_dir
	cmake -DCMAKE_INSTALL_PREFIX=${Dir}/external/eigen-3.3.7/Installation ../
	make install
        cp $(find ${Dir}/external/eigen-3.3.7/Installation -name *.pc) ${Dir}/external/pkgconfig/
fi


# install gsl
if $(pkg-config --exists gsl); then
	echo "GSL library exists."
else
	echo "Install GSL library..."
	cd ${Dir}/external
	wget ftp://ftp.gnu.org/gnu/gsl/gsl-2.5.tar.gz
	tar -zxf gsl-2.5.tar.gz
	cd ${Dir}/external/gsl-2.5/
	mkdir -p Installation
	./configure --prefix=${Dir}/external/gsl-2.5/Installation
	make
	make install
        cp $(find ${Dir}/external/gsl-2.5/Installation -name *.pc) ${Dir}/external/pkgconfig/
fi


# install htslib
if $(pkg-config --exists htslib); then
	echo "htslib library exists."
else
	echo "Install htslib..."
	cd ${Dir}/external
	wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
	tar -xjvf htslib-1.9.tar.bz2
	cd ${Dir}/external/htslib-1.9/
	mkdir -p Installation
	./configure --prefix=${Dir}/external/htslib-1.9/Installation --enable-plugins=no --enable-libcurl=no --enable-s3=no
	make
	make install
        cp $(find ${Dir}/external/htslib-1.9/Installation -name *.pc) ${Dir}/external/pkgconfig/
fi


# install jellyfish
if $(pkg-config --exists jellyfish-2.0); then
	echo "JELLYFISH library exists."
else
	echo "Install JELLYFISH..."
	cd ${Dir}/external
	wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-2.2.10.tar.gz
	tar -zxf jellyfish-2.2.10.tar.gz
	cd ${Dir}/external/jellyfish-2.2.10/
	mkdir -p Installation
	./configure --prefix=${Dir}/external/jellyfish-2.2.10/Installation
	make
	make install
        cp $(find ${Dir}/external/jellyfish-2.2.10/Installation -name *.pc) ${Dir}/external/pkgconfig/
fi


# install clp
if $(pkg-config --exists clp); then
	echo "clp library exists."
else
	echo "Install clp..."
	cd ${Dir}/external
	wget https://www.coin-or.org/download/source/Clp/Clp-1.17.5.tgz
	tar -zxf Clp-1.17.5.tgz
	cd Clp-1.17.5/
	mkdir -p Installation
	./configure -C --prefix=${Dir}/external/Clp-1.17.5/Installation --enable-static
	make
	make install
        cp $(find ${Dir}/external/Clp-1.17.5/Installation -name *.pc) ${Dir}/external/pkgconfig/
fi


echo
echo "****************************************"
echo "* Installation of dependencies done    *"
echo "****************************************"
echo
echo "To configure with CLP, run: ./configure PKG_CONFIG_PATH=${PKG_CONFIG_PATH} BOOST_ROOT=${Dir}/external/boost_1_69_0/Installation"
echo "To configure with gurobi, run: ./configure PKG_CONFIG_PATH=${PKG_CONFIG_PATH} --with-gurobi=<path to gurobi linux64 folder> BOOST_ROOT=${Dir}/external/boost_1_69_0/Installation"
echo
echo "Then compile and install with: make install"