forked from kundajelab/chipseq_pipeline
/
install_dependencies.sh
executable file
·670 lines (560 loc) · 19.1 KB
/
install_dependencies.sh
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################ local installation ##################
if [ "$#" -lt 1 ]
then
SOFTWARE=$HOME/software_bds
else
SOFTWARE=$1
fi
echo
echo "Installation Directory: $SOFTWARE"
echo
# DO NOT CHANGE NAMING OF SOFTWARE DIRECTORY!
BASHRC=$HOME/.bashrc
FLAGDIR=$SOFTWARE/flags
mkdir -p $FLAGDIR
SCRIPTDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
SOFTWARES_APT_GET=(
build-essential
zlib1g-dev
libncurses5-dev
gfortran
openssl
libssl-dev
libfreetype6-dev
liblapack-dev
pkg-config
poppler-utils
libboost-all-dev
graphviz
libcurl4-openssl-dev
libxp6
libgsl0-dev
)
#libboost-all-dev
SOFTWARES_YUM=(
gcc
gcc-c++
kernel-devel
lapack-devel
libXpm-devel
libXp-devel
libXmu-devel
wget
bc
zlib-devel
ncurses-devel
gcc-gfortran
openssl
openssl-devel
freetype-devel
poppler-utils
boost-devel
graphviz
libcurl-devel
libpng-devel
bzip2
gsl-devel
)
#boost-devel
LINUX_ID_LIKE="non-debian,non-fedora"
if [[ $(cat /etc/*-release | grep 'Red Hat\|fedora' | wc -l) > 0 ]]; then
LINUX_ID_LIKE=fedora
fi
if [[ $(cat /etc/*-release | grep debian | wc -l) > 0 ]]; then
LINUX_ID_LIKE=debian
fi
echo
echo Found Linux distribution: ${LINUX_ID_LIKE} based.
echo
echo
echo Checking softwares on your system...
echo
EXIT=0
if [ ${LINUX_ID_LIKE} == debian ]; then
for i in "${SOFTWARES_APT_GET[@]}"; do
if [ $(dpkg -l | awk '{print $2;}' | grep $i | wc -l) != 0 ]; then
echo
echo " * $i found on your system."
else
echo
echo " * $i not found on your system."
echo " Please install $i using the following commmand or ask administrator."
echo " ============================================================="
echo " sudo apt-get install $i"
echo " ============================================================="
EXIT=1
fi
done
elif [ ${LINUX_ID_LIKE} == fedora ]; then
for i in "${SOFTWARES_YUM[@]}"; do
if [ $(rpm -q $i | grep -v "is not installed" | wc -l) != 0 ]; then
echo
echo " * $i found on your system."
else
echo
echo " * $i not found on your system."
echo " Please install $i using the following commmand or ask administrator."
echo " ============================================================="
if [ $i == "lapack-devel" ]; then
echo " # find yum repo for (server-optional) in /etc/yum.repos.d"
echo " grep -rl "server-optional" /etc/yum.repos.d"
echo
echo " # enable the repo (repo name can vary)"
echo " vim /etc/yum.repos.d/[ANY_REPO_FOUND]"
echo
echo " [rhui-REGION-rhel-server-optional]"
echo " ..."
echo " enabled=1"
echo
echo " # install lapack-devel"
echo " sudo yum install lapack-devel"
else
echo " sudo yum install $i"
fi
echo " ============================================================="
EXIT=1
fi
done
else
echo
echo "Your linux system is not based on Fedora (Red Hat, ...) or Debian (Ubuntu, ...)."
echo "Installer will fail if you didn't manually install all required softwares."
echo "List of required softwares: "
echo " gcc, gcc-c++, kernel-devel, lapack-devel, libXpm-devel, libXp-devel, libXmu-devel, wget, bc, zlib-devel, ncurses-devel, gcc-gfortran, openssl, openssl-devel, freetype-devel, poppler-utils, boost-devel, graphviz, libcurl-devel, libpng-devel, bzip2"
fi
if [ $(which git | wc -l) == 0 ]; then
echo
echo " * Git not found on your system."
echo " Please install git using the following commmand or ask administrator."
echo " ============================================================="
if [ ${LINUX_ID_LIKE} == debian ]; then
echo " sudo apt-get install git"
elif [ ${LINUX_ID_LIKE} == fedora ]; then
echo " sudo yum install git"
else
echo " Manually install git on your system"
fi
echo " ============================================================="
echo " You can also install git on your local directory."
echo " (https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)"
EXIT=1
else
echo
echo " * Git found on your system."
fi
NEED_JAVA_INSTALL=0
if [ $(which java | wc -l) == 0 ]; then
echo
echo " * Java not found on your system."
EXIT=1
NEED_JAVA_INSTALL=1
else
JAVA_VER=$(java -version 2>&1 | grep "version" | cut -d'"' -f2 | cut -d'.' -f1-2)
echo
echo " * Java found on your system (version: ${JAVA_VER})."
if [[ (( ${JAVA_VER} < 1.7 )) ]]; then
echo " Java version is too low. Version needs to be >= 1.7"
echo " If you have multiple versions of java installed on your system, choose the latest one."
echo " ============================================================="
echo " sudo update-alternatives --config java"
echo " ============================================================="
EXIT=1
NEED_JAVA_INSTALL=1
fi
fi
if [ ${NEED_JAVA_INSTALL} == 1 ]; then
echo " Please install java using the following commmand or ask administrator."
echo " ============================================================="
if [ ${LINUX_ID_LIKE} == debian ]; then
echo " sudo apt-get install openjdk-8-jre"
echo ""
echo " or"
echo ""
echo " sudo apt-get install openjdk-7-jre"
elif [ ${LINUX_ID_LIKE} == fedora ]; then
echo " sudo yum install java-1.8.0-openjdk"
fi
echo " ============================================================="
echo " You can also install java (jre version >= 1.7) on your local directory."
echo " (http://java.com/en/download/manual.jsp?locale=en)"
fi
if [ $EXIT == 1 ]; then
echo
echo "WARNING!!"
echo
echo "Some of the softwares are not installed on your system."
echo "We strongly recommend to install all softwares listed above and re-run install_dependencies.sh."
echo
echo "However, you can proceed if you have equivalent softwares locally installed on your system."
echo "Otherwise, compilation of some bio-softwares will fail."
echo
echo "If you have trouble with 'sudo apt-get (or yum) install [PACKAGE]', try with 'sudo apt-get (or yum) update' first. "
echo
read -p "Are you sure that you want to proceed? [yes/no] " yn
case $yn in
yes ) echo "YES";;
* ) exit;;
esac
fi
if [ ! -f $BASHRC ]; then
echo > $BASHRC
fi
FAILED=0
function add_to_bashrc {
echo
echo "Adding following lines to your $BASHRC ..."
for i in "${CONTENTS[@]}"; do
if [ $(grep "$i" "$BASHRC" | wc -l ) == 0 ]; then
echo $i
echo $i >> $BASHRC
fi
done
}
function chk_exit_code {
if [ $? == 0 ]; then
echo "." > $1
else
echo
echo =====================================================
echo Installation has failed due to non-zero exit code!
echo =====================================================
echo
echo "Press [Enter] key to continue..."
read -p ""
FAILED=1
fi
}
echo
echo "=============================================================================="
echo "Starting automatic installation for dependencies for ChIP-seq pipeline."
echo "Make sure you have enough disk space (at least 3GB) on your file system."
echo "All dependencies will be installed under $SOFTWARE."
echo "=============================================================================="
echo "Press [Enter] key to continue..."
read -p ""
echo
mkdir -p $SOFTWARE
if [ ! -f $FLAGDIR/BDS ]; then
cd $SOFTWARE
git clone https://github.com/pcingola/BigDataScript
cd BigDataScript
git checkout tags/v0.9999
cp distro/bds_Linux.tgz $HOME
cd $HOME
tar zxvf bds_Linux.tgz
chk_exit_code $FLAGDIR/BDS
cp $SCRIPTDIR/bds.config $HOME/.bds/
CONTENTS=("export PATH=\$PATH:\$HOME/.bds/")
add_to_bashrc
rm -f bds_Linux.tgz
fi
if [ ! -f $FLAGDIR/TABIX ]; then
# local installation for tabix (0.2.6)
cd $SOFTWARE
wget https://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2/download -O tabix-0.2.6.tar.bz2 -N --no-check-certificate
tar jxvf tabix-0.2.6.tar.bz2
rm -f tabix-0.2.6.tar.bz2
cd tabix-0.2.6
make
chk_exit_code $FLAGDIR/TABIX
fi
if [ ! -f $FLAGDIR/BWA ]; then
# Local installation for bwa (0.7.3)
cd $SOFTWARE
git clone https://github.com/lh3/bwa bwa-0.7.3
cd bwa-0.7.3
git checkout tags/0.7.3
make
chk_exit_code $FLAGDIR/BWA
fi
if [ ! -f $FLAGDIR/SAMTOOLS ]; then
# Local installation for samtools (0.1.19)
cd $SOFTWARE
git clone https://github.com/samtools/samtools samtools-0.1.19
cd samtools-0.1.19
git checkout tags/0.1.19
make
chk_exit_code $FLAGDIR/SAMTOOLS
fi
if [ ! -f $FLAGDIR/BEDTOOLS ]; then
# Local installation for bedtools (2.19.1)
cd $SOFTWARE
wget http://pkgs.fedoraproject.org/repo/pkgs/BEDTools/bedtools-2.19.1.tar.gz/58de5377c3fb1bc1ab5a2620cf48f846/bedtools-2.19.1.tar.gz -N
tar zxvf bedtools-2.19.1.tar.gz
rm -f bedtools-2.19.1.tar.gz
cd bedtools2-2.19.1
make
chk_exit_code $FLAGDIR/BEDTOOLS
fi
if [ ! -f $FLAGDIR/UCSCTOOLS ]; then
# Local installation for UCSC tools
cd $SOFTWARE
mkdir -p ucsc_tools
cd ucsc_tools
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig -N
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig -N
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo -N
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedClip -N
chk_exit_code $FLAGDIR/UCSCTOOLS
chmod 755 *
fi
if [ ! -f $FLAGDIR/PICARD ]; then
# Local installation for PICARD tools (1.92)
cd $SOFTWARE
wget http://mitra.stanford.edu/kundaje/software/picard-tools-1.92.tar.gz -N
tar zxvf picard-tools-1.92.tar.gz
rm -f picard-tools-1.92.tar.gz
#wget http://sourceforge.net/projects/picard/files/picard-tools/1.92/picard-tools-1.92.zip/download -O picard-tools-1.92.zip -N
#unzip picard-tools-1.92.zip
#rm -f picard-tools-1.92.zip
chk_exit_code $FLAGDIR/PICARD
cd picard-tools-1.92
chmod 755 *
fi
if [ ! -f $FLAGDIR/PHANTOMPEAKQUALTOOL ]; then
# Local installation for run_spp.R (Anshul's phantompeakqualtool)
cd $SOFTWARE
wget https://phantompeakqualtools.googlecode.com/files/ccQualityControl.v.1.1.tar.gz -N
tar zxvf ccQualityControl.v.1.1.tar.gz
chk_exit_code $FLAGDIR/PHANTOMPEAKQUALTOOL
rm -f ccQualityControl.v.1.1.tar.gz
chmod 755 phantompeakqualtools/*
fi
if [ ! -f $FLAGDIR/R2 ]; then
# Local installation instruction for R (2.15.1) and relevant packages
cd $SOFTWARE
wget http://cran.r-project.org/src/base/R-2/R-2.15.1.tar.gz -N
tar zxvf R-2.15.1.tar.gz
rm -f R-2.15.1.tar.gz
cd R-2.15.1
./configure --with-readline=no --with-x=no --enable-R-static-lib
make
chk_exit_code $FLAGDIR/R2
fi
if [ ! -f $FLAGDIR/R2PACKAGE ]; then
cd $SOFTWARE
wget http://mitra.stanford.edu/kundaje/software/spp_1.13.tar.gz -N
echo > tmp.R
echo 'withCallingHandlers(install.packages("snow", repos="http://cran.us.r-project.org"),warning = function(w) quit(save = "no", status = 1, runLast = FALSE))' >> tmp.R
echo 'withCallingHandlers(install.packages("snowfall", repos="http://cran.us.r-project.org"),warning = function(w) quit(save = "no", status = 1, runLast = FALSE))' >> tmp.R
echo 'withCallingHandlers(install.packages("bitops", repos="http://cran.us.r-project.org"),warning = function(w) quit(save = "no", status = 1, runLast = FALSE))' >> tmp.R
echo 'withCallingHandlers(install.packages("caTools", repos="http://cran.us.r-project.org"),warning = function(w) quit(save = "no", status = 1, runLast = FALSE))' >> tmp.R
echo 'source("http://bioconductor.org/biocLite.R")' >> tmp.R
echo 'biocLite("Rsamtools",suppressUpdates=TRUE)' >> tmp.R
echo 'withCallingHandlers(install.packages("./spp_1.13.tar.gz"),warning = function(w) quit(save = "no", status = 1, runLast = FALSE))' >> tmp.R
$SOFTWARE/R-2.15.1/bin/Rscript tmp.R
chk_exit_code $FLAGDIR/R2PACKAGE
rm -f tmp.R
fi
if [ ! -f $FLAGDIR/LAPACK ]; then
#LAPACK
mkdir -p $SOFTWARE/blas
cd $SOFTWARE/blas
wget http://www.netlib.org/lapack/lapack.tgz -N
tar xzf lapack.tgz
rm -f lapack.tgz
cd lapack-*/
cp INSTALL/make.inc.gfortran make.inc # On Linux with lapack-3.2.1 or newer
make lapacklib
chk_exit_code $FLAGDIR/LAPACK
make clean
fi
if [ ! -f $FLAGDIR/PYTHON2 ]; then
# Local installation instruction for Python (2.7.2) and relevant packages (for macs2)
cd $SOFTWARE
wget https://www.python.org/ftp/python/2.7.2/Python-2.7.2.tgz -N
tar zxvf Python-2.7.2.tgz
rm -f Python-2.7.2.tgz
cd Python-2.7.2
./configure --prefix=$SOFTWARE/python2.7 --enable-unicode=ucs4
make altinstall prefix=$SOFTWARE/python2.7 exec-prefix=$SOFTWARE/python2.7
chk_exit_code $FLAGDIR/PYTHON2
fi
if [ ! -f $FLAGDIR/PIP2 ]; then
ln -s $SOFTWARE/python2.7/bin/python2.7 $SOFTWARE/python2.7/bin/python2
ln -s $SOFTWARE/python2.7/bin/python2.7 $SOFTWARE/python2.7/bin/python
cd $SOFTWARE
cd python2.7/bin
wget https://bootstrap.pypa.io/get-pip.py --no-check-certificate -N
./python2 get-pip.py
$SOFTWARE/python2.7/bin/python2.7 -m pip install --upgrade setuptools
chk_exit_code $FLAGDIR/PIP2
fi
if [ ! -f $FLAGDIR/CYTHON2 ]; then
cd $SOFTWARE/Python-2.7.2
wget http://cython.org/release/Cython-0.22.tar.gz -N
tar zxvf Cython-0.22.tar.gz
cd Cython-0.22
$SOFTWARE/python2.7/bin/python2.7 setup.py install --prefix=$SOFTWARE/python2.7
chk_exit_code $FLAGDIR/CYTHON2
fi
cd $SOFTWARE
if [ ! -f $FLAGDIR/PYTHON2NUMPY ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --install-option="--prefix=$SOFTWARE/python2.7" numpy
chk_exit_code $FLAGDIR/PYTHON2NUMPY
fi
if [ ! -f $FLAGDIR/PYTHON2MATPLOTLIB ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --install-option="--prefix=$SOFTWARE/python2.7" matplotlib
chk_exit_code $FLAGDIR/PYTHON2MATPLOTLIB
fi
if [ ! -f $FLAGDIR/PYTHON2PYSAM ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --install-option="--prefix=$SOFTWARE/python2.7" pysam==0.8.2
chk_exit_code $FLAGDIR/PYTHON2PYSAM
fi
if [ ! -f $FLAGDIR/PYTHON2PYBIGWIG ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --install-option="--prefix=$SOFTWARE/python2.7" pyBigwig
chk_exit_code $FLAGDIR/PYTHON2PYBIGWIG
fi
if [ ! -f $FLAGDIR/PYTHON2SCIPY ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --install-option="--prefix=$SOFTWARE/python2.7" scipy
chk_exit_code $FLAGDIR/PYTHON2SCIPY
fi
if [ ! -f $FLAGDIR/PYTHON2LEVEN ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --install-option="--prefix=$SOFTWARE/python2.7" python-levenshtein
chk_exit_code $FLAGDIR/PYTHON2LEVEN
fi
if [ ! -f $FLAGDIR/PYTHON2DEEP ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --upgrade --install-option="--prefix=$SOFTWARE/python2.7" deeptools==1.5.12
chk_exit_code $FLAGDIR/PYTHON2DEEP
fi
# for atac
if [ ! -f $FLAGDIR/PYTHON2PYBEDTOOLS ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --install-option="--prefix=$SOFTWARE/python2.7" pybedtools
chk_exit_code $FLAGDIR/PYTHON2PYBEDTOOLS
fi
# for atac
if [ ! -f $FLAGDIR/PYTHON2PANDAS ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --install-option="--prefix=$SOFTWARE/python2.7" pandas
chk_exit_code $FLAGDIR/PYTHON2PANDAS
fi
# for atac
if [ ! -f $FLAGDIR/PYTHON2METASEQ ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --install-option="--prefix=$SOFTWARE/python2.7" metaseq
chk_exit_code $FLAGDIR/PYTHON2METASEQ
fi
# for atac
if [ ! -f $FLAGDIR/PYTHON2JINJA2 ]; then
$SOFTWARE/python2.7/bin/python2.7 -m pip install --install-option="--prefix=$SOFTWARE/python2.7" jinja2
chk_exit_code $FLAGDIR/PYTHON2JINJA2
fi
if [ ! -f $FLAGDIR/MACS2 ]; then
# Local installation instruction for MACS2
cd $SOFTWARE
git clone https://github.com/taoliu/MACS/
cd MACS
$SOFTWARE/python2.7/bin/python2.7 setup_w_cython.py install --prefix=$SOFTWARE/python2.7
chk_exit_code $FLAGDIR/MACS2
chmod 755 $SOFTWARE/MACS/bin/*
fi
if [ ! -f $FLAGDIR/DEEPTOOLS ]; then
# deepTools (signal track gen.)
cd $SOFTWARE
rm -rf deepTools
git clone https://github.com/fidelram/deepTools
cd deepTools
git checkout tags/1.5.12
$SOFTWARE/python2.7/bin/python2.7 setup.py install --prefix=$SOFTWARE/python2.7
chk_exit_code $FLAGDIR/DEEPTOOLS
fi
if [ ! -f $FLAGDIR/PYTHON3 ]; then
# Local installation instruction for Python (3.4.3) and relevant packages (for Nathan Boley's IDR)
cd $SOFTWARE
wget https://www.python.org/ftp/python/3.4.3/Python-3.4.3.tgz -N
tar zxvf Python-3.4.3.tgz
rm -f Python-3.4.3.tgz
cd Python-3.4.3
./configure --prefix=$SOFTWARE/python3.4
make altinstall prefix=$SOFTWARE/python3.4 exec-prefix=$SOFTWARE/python3.4
chk_exit_code $FLAGDIR/PYTHON3
ln -s $SOFTWARE/python3.4/bin/python3.4 $SOFTWARE/python3.4/bin/python3
fi
if [ ! -f $FLAGDIR/CYTHON3 ]; then
cd $SOFTWARE/Python-3.4.3
wget http://cython.org/release/Cython-0.22.tar.gz -N
tar zxvf Cython-0.22.tar.gz
cd Cython-0.22
$SOFTWARE/python3.4/bin/python3.4 setup.py install --prefix=$SOFTWARE/python3.4
chk_exit_code $FLAGDIR/CYTHON3
fi
cd $SOFTWARE
if [ ! -f $FLAGDIR/PYTHON3NUMPY ]; then
$SOFTWARE/python3.4/bin/easy_install-3.4 numpy
chk_exit_code $FLAGDIR/PYTHON3NUMPY
fi
if [ ! -f $FLAGDIR/PYTHON3MATPLOTLIB ]; then
$SOFTWARE/python3.4/bin/easy_install-3.4 matplotlib
chk_exit_code $FLAGDIR/PYTHON3MATPLOTLIB
fi
if [ ! -f $FLAGDIR/PYTHON3SCIPY ]; then
$SOFTWARE/python3.4/bin/easy_install-3.4 scipy
chk_exit_code $FLAGDIR/PYTHON3SCIPY
fi
if [ ! -f $FLAGDIR/IDR2 ]; then
# Local installation instruction for IDR2( Nathan Boley's IDR )
cd $SOFTWARE
git clone --recursive https://github.com/nboley/idr.git
cd idr
$SOFTWARE/python3.4/bin/python3.4 setup.py install --prefix=$SOFTWARE/python3.4
chk_exit_code $FLAGDIR/IDR2
fi
if [ ! -f $FLAGDIR/IDR ]; then
# Local installation instruction for Anshul Kundaje's IDR
cd $SOFTWARE
wget https://sites.google.com/site/anshulkundaje/projects/idr/idrCode.tar.gz?attredirects=0 -O idrCode.tar.gz -N
tar zxvf idrCode.tar.gz
chk_exit_code $FLAGDIR/IDR
rm -f idrCode.tar.gz
fi
if [ ! -f $FLAGDIR/GEM ]; then
# Local installation instruction for gem
cd $SOFTWARE
#wget http://cgs.csail.mit.edu/gem/download/gem.v2.6.tar.gz -N
wget http://groups.csail.mit.edu/cgs/gem/download/gem.v2.6.tar.gz -N
tar zxvf gem.v2.6.tar.gz
chk_exit_code $FLAGDIR/GEM
rm -f gem.v2.6.tar.gz
cd gem
chmod 755 $SOFTWARE/gem/*.jar
fi
if [ ! -f $FLAGDIR/WIGGLER ]; then
# Local installation instruction for Wiggler (for generating signal tracks)
cd $SOFTWARE
wget https://align2rawsignal.googlecode.com/files/align2rawsignal.2.0.tgz -N
tar zxvf align2rawsignal.2.0.tgz
chk_exit_code $FLAGDIR/WIGGLER
rm -f align2rawsignal.2.0.tgz
fi
if [ ! -f $FLAGDIR/MCR ]; then
cd $SOFTWARE
wget http://www.broadinstitute.org/~anshul/softwareRepo/MCR2010b.bin -N
chmod 755 MCR2010b.bin
echo '-P installLocation="'$SOFTWARE'/MATLAB_Compiler_Runtime"' > tmp.stdin
./MCR2010b.bin -silent -options "tmp.stdin"
chk_exit_code $FLAGDIR/MCR
rm -f tmp.stdin
rm -f MCR2010b.bin
fi
# for atac
if [ ! -f $FLAGDIR/PRESEQ ]; then
cd $SOFTWARE
rm -rf preseq
git clone https://github.com/smithlabcode/preseq --recursive
cd preseq
git checkout tags/v2.0.2
make
chk_exit_code $FLAGDIR/PRESEQ
fi
# WARNING
if [ $FAILED == 1 ]; then
echo
echo =====================================================
echo "Failed to install some dependencies, check your system requirements and re-run the installer."
echo =====================================================
echo
else
echo
echo =====================================================
echo "Done Installing all dependencies for ChIP-Seq pipeline."
echo =====================================================
echo
fi