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install_dependencies.sh
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install_dependencies.sh
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#!/bin/bash
# last update: 2022/08/21
set -e -o pipefail
#########################
RECOMBINEX_HOME=$(pwd)
BUILD="build"
mainland_china_installation="no";
#########################
timestamp () {
date +"%F %T"
}
clean () {
dir=$1
if [ -d $dir ]
then
echo "remove previously failed installation in $BUILD/$dir"
rm -rf $dir
fi
}
clone () {
url=$1
dir=$(basename $url)
echo "run clone for \"git clone $url\""
git clone $url --depth 1
cd $dir
git fetch --unshallow
}
download () {
url=$1
download_location=$2
echo "Downloading $url to $download_location"
wget -c --no-check-certificate $url -O $download_location
}
tidy_version () {
echo "$1" | awk -F. '{ printf("%d%03d%03d%03d\n", $1,$2,$3,$4); }';
}
check_installed () {
if [ -e "$1/installed" ]; then
echo "installed"
else
echo ""
fi
}
note_installed () {
touch "$1/installed"
}
echo ""
echo ""
echo "##################################################################"
echo "### ###"
echo "### Welcome to RecombineX ###"
echo "### ###"
echo "##################################################################"
echo ""
echo ""
echo "[$(timestamp)] Installation starts ..."
echo ""
if [ -z "$MAKE_JOBS" ]
then
echo "[$(timestamp)] Defaulting to 2 concurrent jobs when executing make. Override with MAKE_JOBS=<NUM>"
MAKE_JOBS=2
echo ""
fi
while getopts ":hc" opt
do
case "${opt}" in
h)
echo "Usage:"
echo "bash install_dependencies.sh"
echo "When installing within mainland China, please run this script with the '-c' option >"
echo "bash install_dependencies.sh -c";;
c)
echo "Detected the '-c' option >"
echo "Set installation location as 'mainland_china'"
mainland_china_installation="yes";;
esac
done
BLAST_VERSION="2.2.31" #
BLAST_DOWNLOAD_URL="http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
RMBLAST_VERSION="2.2.28" #
RMBLAST_DOWNLOAD_URL="http://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/${RMBLAST_VERSION}/ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz"
MUMMER3_VERSION="3.23" # released on 2011.12.17
MUMMER3_DOWNLOAD_URL="https://sourceforge.net/projects/mummer/files/mummer/${MUMMER3_VERSION}/MUMmer${MUMMER3_VERSION}.tar.gz"
# MUMMER4_VERSION="4.0.0beta2" # released on 2017.10.14
# MUMMER4_DOWNLOAD_URL="https://github.com/gmarcais/mummer/releases/download/v${MUMMER4_VERSION}/mummer-${MUMMER4_VERSION}.tar.gz"
# ASSEMBLYTICS_GITHUB_COMMIT_VERSION="df5361f" # committed on 2017.11.02
# ASSEMBLYTICS_DOWNLOAD_URL="https://github.com/MariaNattestad/Assemblytics.git"
# GNUPLOT_VERSION="4.6.6"
# GNUPLOT_DOWNLOAD_URL="https://sourceforge.net/projects/gnuplot/files/gnuplot/${GNUPLOT_VERSION}/gnuplot-${GNUPLOT_VERSION}.tar.gz"
BEDTOOLS_VERSION="2.27.1" # released on 2017.12.14
BEDTOOLS_DOWNLOAD_URL="https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/bedtools-${BEDTOOLS_VERSION}.tar.gz"
SRA_VERSION="3.0.0" # released on 2022.02.10
SRA_DOWNLOAD_URL="http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz"
ART_VERSION="mountrainier2016.06.05" # released on 2016.06.05
ART_DOWNLOAD_URL="https://www.niehs.nih.gov/research/resources/assets/docs/artbin${ART_VERSION}linux64.tgz"
TRIMMOMATIC_VERSION="0.38" #
TRIMMOMATIC_DOWNLOAD_URL="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-${TRIMMOMATIC_VERSION}.zip"
BWA_VERSION="0.7.17" # released on 2017.10.23
BWA_DOWNLOAD_URL="https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2"
SAMTOOLS_VERSION="1.9" # released on 2018.07.18
SAMTOOLS_DOWNLOAD_URL="https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2"
GATK3_VERSION="3.6-6" #
GATK3_DOWNLOAD_URL="https://github.com/yjx1217/GATK3_Archive.git"
# GATK3_DOWNLOAD_URL="https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/GenomeAnalysisTK.jar"
# GATK4_VERSION="4.0.11.0" # released on 2018.10.23
# GATK4_DOWNLOAD_URL="https://github.com/broadinstitute/gatk/releases/download/${GATK4_VERSION}/gatk-${GATK4_VERSION}.zip"
FREEBAYES_VERSION="1.3.4" # released on 20210129
FREEBAYES_SOURCE_DOWNLOAD_URL="https://github.com/freebayes/freebayes/releases/download/v1.3.4/freebayes-1.3.4-src.tar.gz"
FREEBAYES_DOWNLOAD_URL="https://github.com/freebayes/freebayes/releases/download/v${FREEBAYES_VERSION}/freebayes-${FREEBAYES_VERSION}-linux-static-AMD64.gz"
PICARD_VERSION="2.19.0" # released on 2019.03.22
PICARD_DOWNLOAD_URL="https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar"
GEMTOOLS_VERSION="1.7.1" # released on 2013.11.18
GEMTOOLS_DOWNLOAD_URL="http://barnaserver.com/gemtools/releases/GEMTools-static-i3-${GEMTOOLS_VERSION}.tar.gz"
VCFLIB_VERSION="1.0.1" # released on 2019.10.1
VCFLIB_DOWNLOAD_URL="https://github.com/vcflib/vcflib/releases/download/v${VCFLIB_VERSION}/vcflib-${VCFLIB_VERSION}-src.tar.gz"
# VCFTOOLS_VERSION="0.1.16"
# VCFTOOLS_DOWNLOAD_URL="https://github.com/vcftools/vcftools/releases/download/v${VCFTOOLS_VERSION}/vcftools-${VCFTOOLS_VERSION}.tar.gz"
VT_VERSION="" #
VT_GITHUB_COMMIT_VERSION="f6d2b5d" # committed on 2018.08.01
VT_DOWNLOAD_URL="https://github.com/atks/vt"
FREEC_VERSION="11.4" # released on 2018.04.27
FREEC_DOWNLOAD_URL="https://github.com/BoevaLab/FREEC/archive/v${FREEC_VERSION}.tar.gz"
PARALLEL_VERSION="20180722" # released on 2018.07.22
PARALLEL_DOWNLOAD_URL="http://ftp.gnu.org/gnu/parallel/parallel-${PARALLEL_VERSION}.tar.bz2"
# UCSC Utilities
FASPLIT_DOWNLOAD_URL="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSplit"
FATOTWOBIT_DOWNLOAD_URL="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit"
TWOBITINFO_DOWNLOAD_URL="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/twoBitInfo"
if [ -d $BUILD ]
then
echo ""
echo "[$(timestamp)] Detected previously generated $BUILD directory."
else
echo "[$(timestamp)] Create the new $BUILD directory."
mkdir $BUILD
echo ""
fi
cd $BUILD
build_dir=$(pwd)
# Downloading all the dependencies
echo ""
echo "[$(timestamp)] Download and install all the dependencies ..."
# ---------- set Perl & R environment variables -------------
#PYTHONPATH="$build_dir"
PERL5LIB="$build_dir:$PERL5LIB"
PERL5LIB="$build_dir/cpanm/perlmods/lib/perl5:$PERL5LIB"
R_LIBS="$build_dir/R_libs"
R_LIBS_USER="$build_dir/R_libs"
echo ""
echo "PERL5LIB=$PERL5LIB"
echo "R_LIBS=$R_LIBS"
echo "R_LIBS_USER=$R_LIBS_USER"
echo ""
echo "[$(timestamp)] Installing Perl modules ..."
cpanm_dir="$build_dir/cpanm"
if [ -z $(check_installed $cpanm_dir) ]; then
clean $cpanm_dir
mkdir -p $cpanm_dir
cd $cpanm_dir
# wget -c --no-check-certificate -O - https://cpanmin.us/ > cpanm
# work around for the unstable downloading issue
cp $RECOMBINEX_HOME/misc/cpanm .
chmod +x cpanm
mkdir perlmods
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --skip-installed Test::More@1.302086
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --skip-installed Text::Soundex@3.05
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --skip-installed Env@1.04
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --skip-installed Statistics::Descriptive@3.0612
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --skip-installed Statistics::Descriptive::Discrete@0.07
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --skip-installed Math::Random@0.72
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --skip-installed Math::Round@0.07
$cpanm_dir/cpanm -l $cpanm_dir/perlmods --skip-installed Sys::Syslog@0.35
note_installed $cpanm_dir
fi
echo ""
echo "[$(timestamp)] Installing R libraries ..."
rlib_dir="$build_dir/R_libs"
mkdir -p $rlib_dir
cd $rlib_dir
R_VERSION=$(R --version |head -1 |cut -d " " -f 3)
if [ -z $(check_installed "$rlib_dir/optparse") ]; then
clean "$rlib_dir/optparse"
R -e "install.packages(\"optparse\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
note_installed "$rlib_dir/optparse"
fi
if [ -z $(check_installed "$rlib_dir/ggplot2") ]; then
clean "$rlib_dir/ggplot2"
R -e "install.packages(\"ggplot2\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
note_installed "$rlib_dir/ggplot2"
fi
if [ -z $(check_installed "$rlib_dir/scales") ]; then
clean "$rlib_dir/scales"
R -e "install.packages(\"scales\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
note_installed "$rlib_dir/scales"
fi
if [ -z $(check_installed "$rlib_dir/viridis") ]; then
clean "$rlib_dir/viridis"
R -e "install.packages(\"viridis\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\")"
note_installed "$rlib_dir/viridis"
fi
if [ -z $(check_installed "$rlib_dir/DNAcopy") ]; then
clean "$rlib_dir/DNAcopy"
if [ $(tidy_version "$R_VERSION") -ge $(tidy_version "3.6.0") ]
then
echo "R_VERSION=$R_VERSION, use the new bioconductor installation protocol"
R -e ".libPaths(\"$build_dir/R_libs/\");install.packages(\"BiocManager\", repos=\"http://cran.rstudio.com/\", lib=\"$build_dir/R_libs/\");BiocManager::install(\"DNAcopy\", lib=\"$build_dir/R_libs/\")"
else
echo "R_VERSION=$R_VERSION, use the old bioconductor installation protocol"
R -e ".libPaths(\"$build_dir/R_libs/\");source(\"https://bioconductor.org/biocLite.R\");biocLite(\"DNAcopy\", lib=\"$build_dir/R_libs/\", type = \"source\")"
fi
note_installed "$rlib_dir/DNAcopy"
fi
# --------------- ncbi-blast+ ------------------
echo ""
echo "[$(timestamp)] Installing ncbi-blast+ ..."
blast_dir="$build_dir/ncbi-blast-${BLAST_VERSION}+/bin"
windowmasker_dir="$build_dir/ncbi-blast-${BLAST_VERSION}+/bin"
if [ -z $(check_installed $blast_dir) ]; then
cd $build_dir
clean "$build_dir/ncbi-blast-${BLAST_VERSION}+"
echo ""
echo "Installing ncbi-blast+ ..."
echo "Download ncbi-blast-v${BLAST_VERSION}"
download $BLAST_DOWNLOAD_URL "ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
tar xvzf ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
cd $build_dir
rm ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
note_installed $blast_dir
fi
# --------------- ncbi-rmblast ------------------
echo ""
echo "[$(timestamp)] Installing ncbi-rmblast ..."
rmblast_dir="$build_dir/ncbi-rmblastn-${RMBLAST_VERSION}/bin"
if [ -z $(check_installed $rmblast_dir) ]; then
cd $build_dir
clean "$build_dir/ncbi-rmblastn-${RMBLAST_VERSION}"
echo ""
echo "Installing ncbi-rmblastn ..."
echo "Download ncbi-rmblastn-v${BLAST_VERSION}"
download $RMBLAST_DOWNLOAD_URL "ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz"
tar xvzf ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz
# copy rmblastn binary file to ncbi-blast+ directory for easy RepeatMasker configuration
cp $rmblast_dir/rmblastn $blast_dir
cd $build_dir
rm ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz
note_installed $rmblast_dir
fi
# --------------- mummer4 ------------------
# mummer4_dir="$build_dir/mummer-${MUMMER4_VERSION}"
# if [ -z $(check_installed $mummer4_dir) ]; then
# cd $build_dir
# echo "Download mummer-v${MUMMER4_VERSION}"
# download $MUMMER4_DOWNLOAD_URL "mummer-${MUMMER4_VERSION}.tar.gz"
# tar -xzf mummer-${MUMMER4_VERSION}.tar.gz
# echo "$mummer4_dir"
# cd $mummer4_dir
# ./configure
# make -j $MAKE_JOBS
# note_installed $mummer4_dir
# cd ..
# rm mummer-${MUMMER4_VERSION}.tar.gz
# note_installed $mummer4_dir
# fi
# PATH="$mummer4_dir:${PATH}"
# --------------- mummer3 ------------------
echo ""
echo "[$(timestamp)] Installing mummer3 ..."
mummer3_dir="$build_dir/MUMmer${MUMMER3_VERSION}"
if [ -z $(check_installed $mummer3_dir) ]; then
cd $build_dir
clean "$build_dir/MUMmer${MUMMER3_VERSION}"
echo ""
echo "Installing mummer3 ..."
echo "Download mummer-v${MUMMER3_VERSION}"
download $MUMMER3_DOWNLOAD_URL "MUMmer${MUMMER3_VERSION}.tar.gz"
tar xvzf MUMmer${MUMMER3_VERSION}.tar.gz
cd $mummer3_dir
make check
make -j $MAKE_JOBS
PATH=$mummer3_dir:$PATH
cd $build_dir
rm MUMmer${MUMMER3_VERSION}.tar.gz
note_installed $mummer3_dir
fi
# # --------------- ASSEMBLYTICS -----------------
# cd $build_dir
# echo "Download ASSEMBLYTICS-v${ASSEMBLYTICS_VERSION}"
# git clone $ASSEMBLYTICS_DOWNLOAD_URL
# assemblytics_dir="$build_dir/Assemblytics"
# cd $assemblytics_dir
# git checkout -f -q $ASSEMBLYTICS_GITHUB_COMMIT_VERSION
# --------------- bedtools ------------------
echo ""
echo "[$(timestamp)] Installing bedtools ..."
bedtools_dir="$build_dir/bedtools2/bin"
if [ -z $(check_installed $bedtools_dir) ]; then
cd $build_dir
clean "$build_dir/bedtools2"
echo "Download bedtools-v${BEDTOOLS_VERSION}"
download $BEDTOOLS_DOWNLOAD_URL "bedtools-${BEDTOOLS_VERSION}.tar.gz"
tar xvzf bedtools-${BEDTOOLS_VERSION}.tar.gz
cd "$build_dir/bedtools2"
make -j $MAKE_JOBS
cd $build_dir
rm bedtools-${BEDTOOLS_VERSION}.tar.gz
note_installed $bedtools_dir
fi
# ------------- SRA Toolkit -------------------
echo ""
echo "[$(timestamp)] Installing SRA Toolkit ..."
sra_dir="$build_dir/sratoolkit.${SRA_VERSION}-centos_linux64/bin"
if [ -z $(check_installed $sra_dir) ]; then
cd $build_dir
clean "$build_dir/sratoolkit.${SRA_VERSION}-centos_linux64"
echo "Download SRAtoolkit-v${SRA_VERSION}"
download $SRA_DOWNLOAD_URL sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz
tar xvzf sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz
rm sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz
note_installed $sra_dir
fi
# ------------- ART -------------------
echo ""
echo "[$(timestamp)] Installing ART ..."
art_dir="$build_dir/art_bin_MountRainier"
if [ -z $(check_installed $art_dir) ]; then
cd $build_dir
clean "$build_dir/art_bin_MountRainier"
echo "Download ART-v${ART_VERSION}"
download $ART_DOWNLOAD_URL artbin${ART_VERSION}linux64.tgz
tar -zxf artbin${ART_VERSION}linux64.tgz
rm artbin${ART_VERSION}linux64.tgz
note_installed $art_dir
fi
# --------------- Trimmomatic -----------------
echo ""
echo "[$(timestamp)] Installing Trimmomatic ..."
trimmomatic_dir="$build_dir/Trimmomatic-${TRIMMOMATIC_VERSION}"
if [ -z $(check_installed $trimmomatic_dir) ]; then
cd $build_dir
clean "$build_dir/Trimmomatic-${TRIMMOMATIC_VERSION}"
echo "Download Trimmomatic-v${TRIMMOMATIC_VERSION}"
download $TRIMMOMATIC_DOWNLOAD_URL "Trimmomatic-${TRIMMOMATIC_VERSION}.zip"
unzip Trimmomatic-${TRIMMOMATIC_VERSION}.zip
cd $trimmomatic_dir
chmod 755 trimmomatic-${TRIMMOMATIC_VERSION}.jar
ln -s trimmomatic-${TRIMMOMATIC_VERSION}.jar trimmomatic.jar
cd $build_dir
rm Trimmomatic-${TRIMMOMATIC_VERSION}.zip
note_installed $trimmomatic_dir
fi
# ------------- BWA -------------------
echo ""
echo "[$(timestamp)] Installing BWA ..."
bwa_dir="$build_dir/bwa-${BWA_VERSION}"
if [ -z $(check_installed $bwa_dir) ]; then
cd $build_dir
clean "$build_dir/bwa-${BWA_VERSION}"
echo "Download BWA-v${BWA_VERSION}"
download $BWA_DOWNLOAD_URL "bwa-${BWA_VERSION}.tar.bz2"
tar xvjf bwa-${BWA_VERSION}.tar.bz2
cd $bwa_dir
make -j $MAKE_JOBS
cd $build_dir
rm bwa-${BWA_VERSION}.tar.bz2
note_installed $bwa_dir
fi
# --------------- samtools -----------------
echo ""
echo "[$(timestamp)] Installing samtools ..."
samtools_dir="$build_dir/samtools-${SAMTOOLS_VERSION}"
htslib_dir="$samtools_dir/htslib-${SAMTOOLS_VERSION}"
tabix_dir="$samtools_dir/htslib-${SAMTOOLS_VERSION}"
if [ -z $(check_installed $samtools_dir) ]; then
cd $build_dir
clean "$build_dir/samtools-${SAMTOOLS_VERSION}"
echo "Download samtools-v${SAMTOOLS_VERSION}"
download $SAMTOOLS_DOWNLOAD_URL samtools-${SAMTOOLS_VERSION}.tar.bz2
tar xvjf samtools-${SAMTOOLS_VERSION}.tar.bz2
cd $samtools_dir
C_INCLUDE_PATH=""
./configure --without-curses;
make -j $MAKE_JOBS
cd htslib-${SAMTOOLS_VERSION}
#autoheader
#autoconf
./configure
make -j $MAKE_JOBS
cd $build_dir
rm samtools-${SAMTOOLS_VERSION}.tar.bz2
note_installed $samtools_dir
fi
PATH="$samtools_dir:$htslib_dir:$tabix_dir:${PATH}"
# --------------- Picard -----------------
echo ""
echo "[$(timestamp)] Installing picard ..."
picard_dir="$build_dir/Picard-v${PICARD_VERSION}"
if [ -z $(check_installed $picard_dir) ]; then
cd $build_dir
clean "$build_dir/Picard-v${PICARD_VERSION}"
echo "Download Picard-v${PICARD_VERSION}"
download $PICARD_DOWNLOAD_URL "picard.jar"
mkdir Picard-v${PICARD_VERSION}
mv picard.jar $picard_dir
cd $picard_dir
chmod 755 picard.jar
note_installed $picard_dir
fi
# --------------- GATK3 ------------------
echo ""
echo "[$(timestamp)] Installing GATK3 ..."
gatk3_dir="$build_dir/GATK3"
if [ -z $(check_installed $gatk3_dir) ]; then
cd $build_dir
clean "$build_dir/GATK3"
mkdir GATK3
cd GATK3
# download "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/GenomeAnalysisTK.jar" GenomeAnalysisTK.jar
git clone $GATK3_DOWNLOAD_URL
mv ./GATK3_Archive/gatk3.jar.gz .
gunzip gatk3.jar.gz
mv gatk3.jar GenomeAnalysisTK.jar
chmod 755 GenomeAnalysisTK.jar
ln -s GenomeAnalysisTK.jar gatk3.jar
note_installed $gatk3_dir
fi
# # --------------- GATK4 ------------------
# echo ""
# echo "[$(timestamp)] Installing GATK4 ..."
# gatk4_dir="$build_dir/GATK4"
# if [ -z $(check_installed $gatk4_dir) ]; then
# cd $build_dir
# clean "$build_dir/GATK4"
# echo "Download GATK4-v${GATK4_VERSION}"
# download $GATK4_DOWNLOAD_URL "gatk-${GATK4_VERSION}.zip"
# unzip gatk-${GATK4_VERSION}.zip
# mv gatk-${GATK4_VERSION} GATK4
# cd GATK4
# ln -s gatk-package-${GATK4_VERSION}-local.jar gatk4.jar
# cd $build_dir
# rm gatk-${GATK4_VERSION}.zip
# note_installed $gatk4_dir
# fi
# --------------- freebayes ------------------
echo ""
echo "[$(timestamp)] Installing Freebayes ..."
freebayes_dir="$build_dir/freebayes/bin"
if [ -z $(check_installed $freebayes_dir) ]; then
cd $build_dir
clean "$build_dir/freebayes/bin"
echo "Download freebayes-v${FREEBAYES_VERSION}"
download $FREEBAYES_SOURCE_DOWNLOAD_URL freebayes-${FREEBAYES_VERSION}-src.tar.gz
tar xzf freebayes-${FREEBAYES_VERSION}-src.tar.gz
cd freebayes
cd bin
download $FREEBAYES_DOWNLOAD_URL "freebayes-${FREEBAYES_VERSION}-linux-static-AMD64.gz"
gunzip freebayes-${FREEBAYES_VERSION}-linux-static-AMD64.gz
chmod 755 freebayes-${FREEBAYES_VERSION}-linux-static-AMD64
ln -s freebayes-${FREEBAYES_VERSION}-linux-static-AMD64 freebayes
cd $build_dir
rm freebayes-${FREEBAYES_VERSION}-src.tar.gz
note_installed $freebayes_dir
fi
# --------------- GEM-Tools -----------------
echo ""
echo "[$(timestamp)] Installing GEM-Tools ..."
gemtools_dir="$build_dir/gemtools-${GEMTOOLS_VERSION}-i3/bin"
if [ -z $(check_installed $gemtools_dir) ]; then
cd $build_dir
clean "$build_dir/gemtools-${GEMTOOLS_VERSION}-i3"
echo "Download GEMTOOLS-v${GEMTOOLS_VERSION}"
download $GEMTOOLS_DOWNLOAD_URL "gemtools-${GEMTOOLS_VERSION}.tar.gz"
tar zxf "gemtools-${GEMTOOLS_VERSION}.tar.gz"
cd $build_dir
rm gemtools-${GEMTOOLS_VERSION}.tar.gz
note_installed $gemtools_dir
fi
# --------------- VCFlib -----------------
echo ""
echo "[$(timestamp)] Installing VCFlib ..."
vcflib_dir="$build_dir/vcflib-${VCFLIB_VERSION}-src/bin"
if [ -z $(check_installed $vcflib_dir) ]; then
cd $build_dir
clean "$build_dir/vcflib-${VCFLIB_VERSION}-src"
echo "Download VCFlib-v${VCFLIB_VERSION}"
download $VCFLIB_DOWNLOAD_URL vcflib-${VCFLIB_VERSION}-src.tar.gz
tar xvzf vcflib-${VCFLIB_VERSION}-src.tar.gz
cd $build_dir/vcflib-${VCFLIB_VERSION}-src
make
cd $build_dir
rm vcflib-${VCFLIB_VERSION}-src.tar.gz
note_installed $vcflib_dir
fi
# # --------------- vcftools -----------------
# echo ""
# echo "[$(timestamp)] Installing vcftools ..."
# vcftools_dir="$build_dir/vcftools-${VCFTOOLS_VERSION}/build/bin"
# if [ -z $(check_installed $vcflib_dir) ]; then
# cd $build_dir
# clean "$build_dir/vcftools-${VCFTOOLS_VERSION}"
# echo "Download vcftools-v${VCFTOOLS_VERSION}"
# download $VCFTOOLS_DOWNLOAD_URL "vcftools-${VCFTOOLS_VERSION}.tar.gz"
# tar xvzf vcftools-${VCFTOOLS_VERSION}.tar.gz
# cd vcftools-${VCFTOOLS_VERSION}
# mkdir build
# ./configure --prefix="$build_dir/vcftools-${VCFTOOLS_VERSION}/build"
# make -j $MAKE_JOBS
# make install
# cd $build_dir
# rm vcftools-${VCFTOOLS_VERSION}.tar.gz
# note_installed $vcftools_dir
# fi
# ------------------ VT ---------------------
echo ""
echo "[$(timestamp)] Installing VT ..."
vt_dir="$build_dir/vt"
if [ -z $(check_installed $vt_dir) ]; then
cd $build_dir
clean "$build_dir/vt"
echo "Download VT-v${VT_VERSION}"
# git clone $VT_DOWNLOAD_URL
clone $VT_DOWNLOAD_URL
cd $vt_dir
git checkout -f -q $VT_GITHUB_COMMIT_VERSION
make -j $MAKE_JOBS
make test
note_installed $vt_dir
fi
# ----------------- FREEC --------------------
echo ""
echo "[$(timestamp)] Installing FREEC ..."
freec_dir="$build_dir/FREEC-${FREEC_VERSION}"
if [ -z $(check_installed $freec_dir) ]; then
cd $build_dir
clean "$build_dir/FREEC-${FREEC_VERSION}"
echo "Download FREEC-v${FREEC_VERSION}"
download $FREEC_DOWNLOAD_URL "FREEC-${FREEC_VERSION}.tar.gz"
tar xvzf FREEC-${FREEC_VERSION}.tar.gz
cd $freec_dir/src
make -j $MAKE_JOBS
cp freec $freec_dir
cd $freec_dir/scripts
chmod 755 *
cp * $freec_dir
cd $build_dir
rm FREEC-${FREEC_VERSION}.tar.gz
note_installed $freec_dir
fi
# --------------- parallel ------------------
echo ""
echo "[$(timestamp)] Installing parallel ..."
parallel_dir="$build_dir/parallel-${PARALLEL_VERSION}/bin"
if [ -z $(check_installed $parallel_dir) ]; then
cd $build_dir
clean "$build_dir/parallel-${PARALLEL_VERSION}"
echo "Download parallel-${PARALLEL_VERSION}"
download $PARALLEL_DOWNLOAD_URL "parallel_v${PARALLEL_VERSION}.tar.bz2"
tar xvjf parallel_v${PARALLEL_VERSION}.tar.bz2
cd parallel-${PARALLEL_VERSION}
./configure --prefix="$build_dir/parallel-${PARALLEL_VERSION}"
make -j $MAKE_JOBS
make install
parallel_dir="$build_dir/parallel-${PARALLEL_VERSION}/bin"
cd ..
rm parallel_v${PARALLEL_VERSION}.tar.bz2
note_installed $parallel_dir
fi
# --------------- UCSC Utilities -----------------
echo ""
echo "[$(timestamp)] Installing UCSC Utilities ..."
ucsc_dir="$build_dir/UCSC_Utilities"
if [ -z $(check_installed $ucsc_dir) ]; then
cd $build_dir
clean "$build_dir/UCSC_Utilities"
mkdir UCSC_Utilities
cd $ucsc_dir
download $FASPLIT_DOWNLOAD_URL "faSplit"
download $FATOTWOBIT_DOWNLOAD_URL "faToTwoBit"
download $TWOBITINFO_DOWNLOAD_URL "twoBitInfo"
chmod 755 $ucsc_dir/*
note_installed $ucsc_dir
fi
# Configure executable paths
cd $RECOMBINEX_HOME
echo ""
echo "[$(timestamp)] Configuring executable paths ..."
echo "export RECOMBINEX_HOME=${RECOMBINEX_HOME}" > env.sh
echo "export build_dir=${build_dir}" >> env.sh
echo "export PERL5LIB=${PERL5LIB}" >> env.sh
echo "export R_LIBS=${R_LIBS}" >> env.sh
echo "export cpanm_dir=${cpanm_dir}" >> env.sh
echo "export blast_dir=${blast_dir}" >> env.sh
echo "export rmblast_dir=${rmblast_dir}" >> env.sh
echo "export windowmasker_dir=${windowmasker_dir}" >> env.sh
# echo "export mummer4_dir=${mummer4_dir}" >> env.sh
echo "export mummer3_dir=${mummer3_dir}" >> env.sh
# echo "export assemblytics_dir=${assemblytics_dir}" >> env.sh
# echo "export gnuplot_dir=${gnuplot_dir}" >> env.sh
echo "export bedtools_dir=${bedtools_dir}" >> env.sh
echo "export sra_dir=${sra_dir}" >> env.sh
echo "export art_dir=${art_dir}" >> env.sh
echo "export trimmomatic_dir=${trimmomatic_dir}" >> env.sh
echo "export bwa_dir=${bwa_dir}" >> env.sh
echo "export samtools_dir=${samtools_dir}" >> env.sh
echo "export picard_dir=${picard_dir}" >> env.sh
echo "export gatk3_dir=${gatk3_dir}" >> env.sh
# echo "export gatk4_dir=${gatk4_dir}" >> env.sh
echo "export freebayes_dir=${freebayes_dir}" >> env.sh
echo "export gemtools_dir=${gemtools_dir}" >> env.sh
echo "export vcflib_dir=${vcflib_dir}" >> env.sh
# echo "export vcftools_dir=${vcftools_dir}" >> env.sh
echo "export vt_dir=${vt_dir}" >> env.sh
echo "export freec_dir=${freec_dir}" >> env.sh
echo "export parallel_dir=${parallel_dir}" >> env.sh
echo "export ucsc_dir=${ucsc_dir}" >> env.sh
# test java configuration: requireds java 1.8
echo ""
echo "##########################################"
echo "Testing java configuration ..."
echo ""
java_bin=""
if type -p java
then
java_bin=$(which java)
echo "found java executable in PATH: $java_bin"
elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]]
then
java_bin="$JAVA_HOME/bin/java"
echo "found java executable in JAVA_HOME: $java_bin"
else
echo "";
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";
echo "Failed to detect Java installation in the system!"
echo "Please install java 1.8, which is a dependency of RecombineX!\n";
echo "After the java installation, please manually set the directory path to java 1.8 executable on the last line of the env.sh file generated by this installation script!"
echo "export java_dir=" >> env.sh
fi
if [[ -n "$java_bin" ]]
then
java_version=$("$java_bin" -version 2>&1 | awk -F '"' '/version/ {print $2}')
echo "detected java_version: $java_version"
if [ $(tidy_version "$java_version") -eq $(tidy_version "1.8") ]
then
java_dir=$(dirname $java_bin)
echo "export java_dir=${java_dir}" >> env.sh
echo "You have the correct java version for RecombineX! RecombineX will take care of the configuration."
else
echo "";
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";
echo "Your java version is not the version required by RecombineX (java v1.8)!"
echo "Please manually set the directory path to java 1.8 executable on the last line of the env.sh file generated by this installation script!"
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";
echo "export java_dir=" >> env.sh
fi
fi
echo ""
echo "[$(timestamp)] Uncompress large supporting files ..."
gunzip $RECOMBINEX_HOME/data/S288C.all_feature.gff.gz
gunzip $RECOMBINEX_HOME/data/S288C.genome.fa.gz
gunzip $RECOMBINEX_HOME/data/SK1.all_feature.gff.gz
gunzip $RECOMBINEX_HOME/data/SK1.genome.fa.gz
gunzip $RECOMBINEX_HOME/data/P1-P2.ref.final.SNP.markers.txt.gz
gunzip $RECOMBINEX_HOME/data/ref.centromere.relabel.gff.gz
gunzip $RECOMBINEX_HOME/data/ref.genome.raw.relabel.fa.gz
echo "[$(timestamp)] Done!"
echo ""
echo ""
echo "#################### IMPORTANT !!! #######################"
echo ""
echo "[$(timestamp)] Automatic dependencies installation finished! "
echo ""
echo "#########################################################"
############################
# checking Bash exit status
if [ $? -eq 0 ]
then
echo ""
echo "RecombineX message: This bash script has been successfully processed! :)"
echo ""
echo ""
exit 0
fi
############################