INSTALL

#!/bin/bash
#@(#)INSTALL  2024-07-12  A.J.Travis

#
# Install "hyb" under Ubuntu 20.04 LTS
#

# check if package is installed
installed() {
    return $(dpkg-query -W -f '${Status}\n' "${1}" 2>&1|awk '/ok installed/{print 0;exit}{print 1}')
}

pkgs=(wget libpng-dev flexbar bowtie2 make gcc unzip ncbi-blast+ fastqc gdebi-core rnahybrid rsync)
for pkg in ${pkgs[@]}; do
    if ! $(installed $pkg) ; then
        echo sudo apt install -y $pkg
    fi
done

# GitHub repository
export GITHUB=https://github.com/gkudla/hyb

# installation directory
if [ $USER == root ]; then
    export HYB_HOME=/usr/local/hyb
else
    export HYB_HOME=${HOME}/hyb
fi

# set PATH for "hyb" test run
export PATH=${HYB_HOME}/bin:$PATH
echo "Please add ${HYB_HOME}/bin to your PATH after running the INSTALL script"
echo "(press any key to continue...)"
read -n 1 key; echo

# download directory must be writeable
dir=$(pwd)
if [ ! -w ${dir} ]; then
    echo "$0: can't write to ${dir}"
    exit 1
fi

# check if "hyb" is already installed
if [ -e ${HYB_HOME} ]; then
    echo "$0: ${HYB_HOME} already exists - replace it?"
    read -n 1 key; echo
    if [ "$key" == "y" ]; then
        rm -r ${HYB_HOME}
    else
        echo "$0: installation cancelled"
        exit 1
    fi
fi

# install hyb files
mkdir -p ${HYB_HOME}
rsync -axHP bin lib man data ${HYB_HOME}

# download and compile BLAT (requires libpng-dev)
wget -nc http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip
unzip blatSrc35.zip
export MACHTYPE=$(arch)
mkdir -p ${HOME}/bin/${MACHTYPE}
cd blatSrc
make

# move to BLAT installation directory
if [ $USER == root ]; then
    mv -i ${HOME}/bin/${MACHTYPE}/* /usr/local/bin/
else
    export PATH=${HOME}/bin/${MACHTYPE}:${PATH}
fi

# build databases
cd ${HYB_HOME}/data/db
make

# UNAfold
if [ ! -x "$(which hybrid-min)" ]; then
    if [ $USER == root ]; then
        wget http://www.unafold.org/download/oligoarrayaux-3.8.tar.bz2
	tar xf oligoarrayaux-3.8.tar.bz2
	cd oligoarrayaux-3.8
	make install
    else
        echo "$0: install bio-linux-oligoarrayaux to test hyb"
        exit 1
    fi
fi

# Vienna RNA
if [ ! -x "$(which RNAfold)" ]; then
    if [ $USER == root ]; then
        wget https://www.tbi.univie.ac.at/RNA/download/ubuntu/ubuntu_20_04/viennarna_2.5.1-1_amd64.deb
        gdebi viennarna_2.5.1-1_amd64.deb
    else
        echo "$0: install Vienna RNA to test hyb"
        exit 1
    fi
fi

# test
cd ${HYB_HOME}/data/fastq
hyb analyse in=testdata.txt db=hOH7

# finished
exit 0