#!/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 () {

}

clone () {

}

download () {

}

tidy_version () {

echo "$1" | awk -F. '{ printf("%d%03d%03d%03d\n", $1,$2,$3,$4); }';

}

check_installed () {

}

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

############################