/
install_dependencies.sh
executable file
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/
install_dependencies.sh
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#!/bin/bash
set -e
set -x
start_dir=$(pwd)
KMC_VERSION=3.0.0
MUMMER_VERSION=3.23
SAMTOOLS_VERSION=${SAMTOOLS_VERSION:-"1.3"}
SMALT_VERSION=0.7.6
#KMC_DOWNLOAD_URL=http://sun.aei.polsl.pl/REFRESH/kmc/downloads/${KMC_VERSION}/linux/kmc
#KMCDUMP_DOWNLOAD_URL=http://sun.aei.polsl.pl/REFRESH/kmc/downloads/${KMC_VERSION}/linux/kmc_dump
KMC3_DOWNLOAD_URL="https://github.com/refresh-bio/KMC/releases/download/v${KMC_VERSION}/KMC3.linux.tar.gz"
MUMMER_DOWNLOAD_URL="http://downloads.sourceforge.net/project/mummer/mummer/${MUMMER_VERSION}/MUMmer${MUMMER_VERSION}.tar.gz"
SAMTOOLS_DOWNLOAD_URL="https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2"
SMALT_DOWNLOAD_URL=http://downloads.sourceforge.net/project/smalt/smalt-${SMALT_VERSION}-bin.tar.gz
# Make an install location
if [ ! -d 'build' ]; then
mkdir build
fi
cd build
build_dir=$(pwd)
# DOWNLOAD ALL THE THINGS
download () {
url=$1
download_location=$2
if [ -e $download_location ]; then
echo "Skipping download of $url, $download_location already exists"
else
echo "Downloading $url to $download_location"
wget $url -O $download_location
fi
}
# --------------- kmc -----------------
kmc_dir="$build_dir/kmc-${KMC_VERSION}"
rm -fr $kmc_dir
mkdir $kmc_dir
cd $kmc_dir
#download $KMC3_DOWNLOAD_URL "kmc"
#download $KMCDUMP_DOWNLOAD_URL "kmc_dump"
#chmod +x kmc kmc_dump
download "${KMC3_DOWNLOAD_URL}" "KMC3.linux.tar.gz"
tar xzf KMC3.linux.tar.gz
chmod +x kmc
chmod +x kmc_tools
chmod +x kmc_dump
# --------------- mummer ------------------
cd $build_dir
download $MUMMER_DOWNLOAD_URL "MUMmer${MUMMER_VERSION}.tar.gz"
mummer_dir="$build_dir/MUMmer${MUMMER_VERSION}"
tar -zxf MUMmer${MUMMER_VERSION}.tar.gz
cd $mummer_dir
make
# --------------- samtools -----------------
cd $build_dir
download $SAMTOOLS_DOWNLOAD_URL "samtools-${SAMTOOLS_VERSION}.tar.bz2"
samtools_dir="$build_dir/samtools-${SAMTOOLS_VERSION}"
tar -xjf samtools-${SAMTOOLS_VERSION}.tar.bz2
cd $samtools_dir
make
# --------------- smalt -----------------
cd $build_dir
download $SMALT_DOWNLOAD_URL "smalt-${SMALT_VERSION}-bin.tar.gz"
tar zxf smalt-${SMALT_VERSION}-bin.tar.gz
smalt_dir="$build_dir/smalt-${SMALT_VERSION}-bin"
cd $smalt_dir
ln -fs smalt_x86_64 smalt
cd $start_dir
update_path () {
new_dir=$1
if [[ ! "$PATH" =~ (^|:)"${new_dir}"(:|$) ]]; then
export PATH=${new_dir}:${PATH}
fi
}
update_path ${kmc_dir}
update_path ${mummer_dir}
update_path ${samtools_dir}
update_path ${smalt_dir}
pip install cython