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install_software.sh
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install_software.sh
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##########################################################################################################################
# INSTALL SOFTWARE NECESSARY FOR running HybPhyloMaker #
# and clone HybPhyloMaker GitHub repository (incl. test dataset) #
# This should work on major Linux distribution (tested on Debian, Ubuntu, OpenSUSE, Fedora, CentOS and Scientific Linux) #
# Without changes works only on 64-bit platforms (x86_64) #
# This script MUST be run with root privileges! #
# #
# Tomas Fer, 2017, 2018, 2019, 2020, 2021 #
# tomas.fer@natur.cuni.cz #
# https://github.com/tomas-fer/HybPhyloMaker #
# v.1.8.0f #
##########################################################################################################################
#Carefully set your distribution
distribution=Debian #one of: Debian (also for Ubuntu), OpenSUSE, Fedora, CentOS (also for Scientific Linux)
#Change name of your default package management tool (apt-get on Debian/Ubuntu, zypper on OpenSUSE, yum on Fedora/CentOS/Scientific/RHEL)
installer=apt-get #one of: apt-get, zypper, yum
echo -e "\n************************************************"
echo -e "Installation script for HybPhyloMaker is running"
echo -e "All necessary software will be installed."
echo -e "See installation logs in 'install' folder.\n"
echo -e "Your distribution: $distribution"
echo -e "Your package manager: $installer"
echo -e "************************************************\n"
mkdir -p install
cd install
#------INSTALL SOFTWARE FROM REPOSITORIES------
#Install software using default package manager specified above
#Compilation utilities, i.e., gcc, g++, make, autoconf
if [[ $distribution =~ "Debian" ]]; then
for i in gcc g++ make automake cmake; do
if ! [ -x "$(command -v $i)" ]; then
echo -e "Installing '$i'"
$installer install -y $i &> ${i}_install.log
fi
done
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]] || [[ $distribution =~ "OpenSUSE" ]]; then
for i in make automake cmake; do
if ! [ -x "$(command -v $i)" ]; then
echo -e "Installing '$i'"
$installer install -y $i &> ${i}_install.log
fi
done
if ! [ -x "$(command -v gcc)" ]; then
echo -e "Installing 'gcc'"
$installer install -y gcc &> gcc_install.log
fi
if ! [ -x "$(command -v g++)" ]; then
echo -e "Installing 'g++'"
$installer install -y gcc-c++ &> g++_install.log
fi
fi
if ! [ -x "$(command -v autoconf)" ]; then
echo -e "Installing 'autoconf'"
$installer install -y autoconf &> autoconf_install.log
fi
if ! [ -x "$(command -v autoreconf)" ]; then
echo -e "Installing 'dh-autoreconf'"
$installer install -y dh-autoreconf &> dh-autoreconf_install.log
fi
#Perl
if ! [ -x "$(command -v perl)" ]; then
echo -e "Installing 'perl'"
$installer install -y perl &> perl_install.log
fi
#Python2
if ! [ -x "$(command -v python2)" ]; then
echo -e "Installing 'python2'"
if [[ $distribution =~ "Fedora" ]]; then
$installer install -y python27 &> python_install.log
else
$installer install -y python &> python_install.log
fi
fi
#Python3
if [[ $distribution =~ "Debian" ]]; then
if [ ! "$(dpkg -s python3-dev 2>/dev/null | grep -w "ok")" ]; then
echo -e "Installing 'python3'"
$installer install -y python3-dev &> python3_install.log
fi
elif [[ $distribution =~ "CentOS" ]]; then
if [ ! "$(rpm -qa | grep python3-devel)" ]; then
echo -e "Installing 'python3'"
$installer install -y epel-release &> python3_install.log #Only for CentOS
$installer install -y python3-devel &>> python3_install.log #Only for CentOS
fi
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "OpenSUSE" ]]; then
if [ ! "$(rpm -qa | grep python3-devel)" ]; then
echo -e "Installing 'python3'"
$installer install -y python3-devel &> python3_install.log
fi
fi
#Pip2
if [[ $distribution =~ "Debian" ]]; then
if ! [ -x "$(command -v pip2)" ]; then
echo -e "Installing 'pip2'"
#$installer install -y python-pip &> pip_install.log
wget https://bootstrap.pypa.io/pip/2.7/get-pip.py &> pip_install.log
python2 get-pip.py &>> pip_install.log
fi
#pip2 install --upgrade pip &>> pip_install.log #the upgrade makes troubles on Debian/Ubuntu
echo >/dev/null
else
if ! [ -x "$(command -v pip2.7)" ]; then
echo -e "Installing 'pip2'"
#$installer install -y python-pip &> pip_install.log
python2 -m ensurepip --upgrade
fi
#pip2.7 install --upgrade pip &>> pip_install.log #the upgrade makes troubles on Debian/Ubuntu
echo >/dev/null
fi
#Pip3 (also required for 'biopython', 'kindel' and 'p4' installation, see below)
if ! [ -x "$(command -v pip3)" ]; then
if [[ $distribution =~ "CentOS" ]]; then
echo -e "Installing 'pip3'"
$installer install -y python34-devel &>> python3_install.log #Only for CentOS, older version?
$installer install -y python3-devel &>> python3_install.log #Only for CentOS
$installer install -y python34-pip &> pip3_install.log #Only for CentOS, older version?
$installer install -y python3-pip &> pip3_install.log #Only for CentOS
elif [[ $distribution =~ "Debian" ]]; then
echo -e "Installing 'pip3'"
$installer install -y python3-dev &>> python3_install.log #Does not work on CentOS
$installer install -y python3-pip &> pip3_install.log #Does not work on CentOS
elif [[ $distribution =~ "OpenSUSE" ]] || [[ $distribution =~ "Fedora" ]]; then
echo -e "Installing 'pip3'"
$installer install -y python3-devel &>> python3_install.log #Does not work on CentOS
$installer install -y python3-pip &> pip3_install.log #Does not work on CentOS
fi
fi
if [[ $distribution =~ "Fedora" ]]; then
#python3 -m pip install --upgrade pip &>> pip3_install.log #the upgrade makes troubles on Debian/Ubuntu
echo >/dev/null
else
#pip3 install --upgrade pip &>> pip3_install.log #the upgrade makes troubles on Debian/Ubuntu
echo >/dev/null
fi
#Biopython
if [ ! `python3 -c "import Bio; print(Bio.__version__)" 2>/dev/null` ]; then
echo -e "Installing 'biopython for python3'"
pip3 install biopython &> biopython_install.log
fi
#Java
if ! [ -x "$(command -v java)" ]; then
if [[ $distribution =~ "Debian" ]]; then
echo -e "Installing 'java'"
distrib=$(cat /etc/*release | grep ^ID= | cut -d'=' -f2)
if [[ $distrib =~ "debian" ]]; then
debver=$(cat /etc/debian_version | cut -d"." -f1)
if [ "$debver" -eq "9" ]; then
$installer install -y openjdk-8-jdk &> java_install.log #Debian9/Ubuntu
elif [ "$debver" -gt "9" ]; then
$installer install -y openjdk-11-jdk &> java_install.log #Debian9/Ubuntu
else
$installer install -y openjdk-7-jdk &> java_install.log #Debian9/Ubuntu
fi
elif [[ $distrib =~ "ubuntu" ]]; then
#ubuver=$(lsb_release -r -s | cut -d"." -f1)
ubuver=$(grep -Po '(?<=VERSION_ID=")\d+' /etc/os-release)
if [ "$ubuver" -ge "16" ]; then
$installer install -y openjdk-8-jdk &> java_install.log #Debian9/Ubuntu
else
$installer install -y openjdk-7-jdk &> java_install.log #Debian9/Ubuntu
fi
fi
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
echo -e "Installing 'java'"
$installer install -y java-1.8.0-openjdk-devel.x86_64 &> java_install.log #Fedora/CentOS
elif [[ $distribution =~ "OpenSUSE" ]]; then
susever=$(cat /etc/*release | grep ^VERSION_ID= | cut -d'=' -f2 | sed 's/\"//g' | cut -d'.' -f1)
echo -e "Installing 'java'"
if [ "$susever" -gt "12" ]; then
$installer install -y java-1_8_0-openjdk-devel &> java_install.log #OpenSUSE
else
$installer install -y java-1_7_0-openjdk-devel &> java_install.log #OpenSUSE
fi
fi
fi
#libpng library
if [ ! "$(whereis libpng | grep /)" ]; then
if [[ $distribution =~ "Debian" ]]; then
echo -e "Installing 'libpng'"
$installer install -y libpng-dev &> libpng_install.log #Debian/Ubuntu
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]] || [[ $distribution =~ "OpenSUSE" ]]; then
echo -e "Installing 'libpng'"
$installer install -y libpng-devel &> libpng_install.log #Fedora/CentOS/OpenSUSE
fi
fi
#zlib library
if [ ! "$(whereis zlib | grep /)" ]; then
if [[ $distribution =~ "Debian" ]]; then
echo -e "Installing 'zlib'"
$installer install -y zlib1g-dev &>> zlib_install.log #Debian/Ubuntu
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]] || [[ $distribution =~ "OpenSUSE" ]]; then
echo -e "Installing 'zlib'"
$installer install -y zlib-devel &>> zlib_install.log #Fedora/CentOS/OpenSUSE
fi
fi
#libbzip2 library
if [ ! "$(whereis libbz2 | grep /)" ]; then
if [[ $distribution =~ "Debian" ]]; then
echo -e "Installing 'libbz2'"
$installer install -y libbz2-dev &>> libbz2_install.log #Debian/Ubuntu
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
echo -e "Installing 'libbz2'"
$installer install -y bzip2-devel &>> libbz2_install.log #Fedora/CentOS
elif [[ $distribution =~ "OpenSUSE" ]]; then
echo -e "Installing 'libbz2'"
$installer install -y libbz2-devel &>> libbz2_install.log #OpenSUSE
fi
fi
#lzma library
if [[ $distribution =~ "Debian" ]]; then
if [ ! "$(dpkg -s liblzma-dev 2>/dev/null | grep -w "ok")" ]; then
echo -e "Installing 'lzma'"
$installer install -y liblzma-dev &>> lzma_install.log #Debian/Ubuntu
fi
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]] || [[ $distribution =~ "OpenSUSE" ]]; then
if [ ! "$(rpm -qa | grep xz-devel)" ]; then
echo -e "Installing 'lzma'"
$installer install -y xz-devel &>> lzma_install.log #Fedora/CentOS/OpenSUSE
fi
fi
#pkg-config
if [ ! "$(whereis pkg-config | grep /)" ]; then
if [[ $distribution =~ "Debian" ]] || [[ $distribution =~ "OpenSUSE" ]]; then
echo -e "Installing 'pkg-config'"
$installer install -y pkg-config &> pkg-config_install.log #Debian/Ubuntu/OpenSUSE
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
echo -e "Installing 'pkg-config'"
$installer install -y pkgconfig &> pkg-config_install.log #Fedora/CentOS
fi
fi
#libtool
if [ ! "$(whereis libtool | grep /)" ]; then
echo -e "Installing 'libtool'"
$installer install -y libtool &> libtool_install.log
fi
#unzip
if [ ! "$(whereis unzip | grep /)" ]; then
echo -e "Installing 'unzip'"
$installer install -y unzip &> unzip_install.log
fi
#wget, tar, bzip2, bc, git
for i in wget tar bzip2 bc git; do
if ! [ -x "$(command -v $i)" ]; then
echo -e "Installing '$i'"
$installer install -y $i &> ${i}_install.log
fi
done
#R
#Comment for Ubuntu/Debian: you should install the newest version of R by adding CRAN mirror to /etc/apt/sources.list
#Look at the end of this script for an advice how to do that...
#Newer version (i.e., at least v3.3) should be installed before running this script!
if ! [ -x "$(command -v R)" ]; then
if [[ $distribution =~ "Debian" ]]; then
echo -e "Installing 'R'"
$installer install -y r-base-dev &> R_install.log #Debian/Ubuntu
$installer install -y gfortran &> gfortran_install.log #Debian/Ubuntu
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
echo -e "Installing 'R'"
$installer install -y R &> R_install.log #Fedora/CentOS
$installer install -y gcc-gfortran &> gfortran_install.log #Fedora/CentOS
elif [[ $distribution =~ "OpenSUSE" ]]; then
echo -e "Installing 'R'"
$installer install -y R-base-devel &> R_install.log #OpenSUSE
$installer install -y gcc-fortran &> gfortran_install.log #necessary in OpenSUSE for compilation of some R packages
fi
fi
#R packages
for Rpackage in ape seqinr data.table openxlsx phytools; do
R -q -e "is.element('$Rpackage', installed.packages()[,1])" > testpackage
if grep -Fxq "[1] FALSE" testpackage; then
echo -e "Installing '$Rpackage for R'"
R -q -e "install.packages('$Rpackage', repos='http://cran.rstudio.com/')" &> R_${Rpackage}_install.log
else
echo -e "R package $Rpackage already installed"
fi
done
rm testpackage
#R package phangorn (requires quadprog, igraph, fastmatch) - for neighbour network
#older version installed due to compatibility with R 3.5
for Rpackage in quadprog igraph fastmatch; do
R -q -e "is.element('$Rpackage', installed.packages()[,1])" > testpackage
if grep -Fxq "[1] FALSE" testpackage; then
echo -e "Installing '$Rpackage for R'"
R -q -e "install.packages('$Rpackage', repos='http://cran.rstudio.com/')" &> R_${Rpackage}_install.log
else
echo -e "R package $Rpackage already installed"
fi
done
rm testpackage
R -q -e "is.element('phangorn', installed.packages()[,1])" > testpackage
if grep -Fxq "[1] FALSE" testpackage; then
echo -e "Installing 'phangorn for R'"
wget https://cran.r-project.org/src/contrib/Archive/phangorn/phangorn_2.5.5.tar.gz &> R_phangorn_install.log
R CMD INSTALL phangorn_2.5.5.tar.gz &>> R_phangorn_install.log
rm phangorn_2.5.5.tar.gz
else
echo -e "R package phangorn already installed"
fi
rm testpackage
#R package treeio (from Bioconductor) - for Astral -t 4
for Rpackage in rvcheck tidytree rlang jsonlite; do
R -q -e "is.element('$Rpackage', installed.packages()[,1])" > testpackage
if grep -Fxq "[1] FALSE" testpackage; then
echo -e "Installing '$Rpackage for R'"
R -q -e "install.packages('$Rpackage', repos='http://cran.rstudio.com/')" &> R_${Rpackage}_install.log
else
echo -e "R package $Rpackage already installed"
fi
done
rm testpackage
R -q -e "is.element('treeio', installed.packages()[,1])" > testpackage
if grep -Fxq "[1] FALSE" testpackage; then
echo -e "Installing 'treeio for R'"
wget https://www.bioconductor.org/packages/3.7/bioc/src/contrib/treeio_1.4.3.tar.gz &> R_treeio_install.log
R CMD INSTALL treeio_1.4.3.tar.gz &>> R_treeio_install.log
rm treeio_1.4.3.tar.gz
else
echo -e "R package treeio already installed"
fi
rm testpackage
#R package gplots (requires caTools, bitops, gdata) - for hetmap.R
#older version installed due to compatibility with R 3.5
for Rpackage in bitops gdata; do
R -q -e "is.element('$Rpackage', installed.packages()[,1])" > testpackage
if grep -Fxq "[1] FALSE" testpackage; then
echo -e "Installing '$Rpackage for R'"
R -q -e "install.packages('$Rpackage', repos='http://cran.rstudio.com/')" &> R_${Rpackage}_install.log
else
echo -e "R package $Rpackage already installed"
fi
done
rm testpackage
R -q -e "is.element('caTools', installed.packages()[,1])" > testpackage
if grep -Fxq "[1] FALSE" testpackage; then
echo -e "Installing 'caTools for R'"
wget https://cran.r-project.org/src/contrib/Archive/caTools/caTools_1.17.1.4.tar.gz &> R_caTools_install.log
R CMD INSTALL caTools_1.17.1.4.tar.gz &>> R_caTools_install.log
rm caTools_1.17.1.4.tar.gz
else
echo -e "R package caTools already installed"
fi
rm testpackage
R -q -e "is.element('gplots', installed.packages()[,1])" > testpackage
if grep -Fxq "[1] FALSE" testpackage; then
echo -e "Installing 'gplots for R'"
wget https://cran.r-project.org/src/contrib/Archive/gplots/gplots_3.0.1.2.tar.gz &> R_gplots_install.log
R CMD INSTALL gplots_3.0.1.2.tar.gz &>> R_gplots_install.log
rm gplots_3.0.1.2.tar.gz
else
echo -e "R package gplots already installed"
fi
rm testpackage
##------UNCOMMENT NEXT LINES (the whole block) IF YOU WISH TO INSTALL THIS SOFTWARE FROM REPOSITORIES------
#If commented then newest versions will be installed later from source, see below
# if [[ $distribution =~ "Debian" ]]; then
# $installer install -y parallel #Debian/Ubuntu/Fedora
# $installer install -y bowtie2 #Debian/Ubuntu
# $installer install -y samtools #Debian/Ubuntu/CentOS/Fedora
# $installer install -y fastx-toolkit #Debian/Ubuntu
# $installer install -y mafft #Debian/Ubuntu
# $installer install -y fasttree #Debian/Ubuntu
# elif [[ $distribution =~ "OpenSUSE" ]]; then
# $installer install -y gnu_parallel #OpenSUSE
# elif [[ $distribution =~ "Fedora" ]]; then
# $installer install -y parallel #Debian/Ubuntu/Fedora
# $installer install -y samtools #Debian/Ubuntu/CentOS/Fedora
# $installer install -y fastx_toolkit #Fedora; if commented newest version will be installed later from source, see below
# elif [[ $distribution =~ "CentOS" ]]; then
# $installer install -y samtools #Debian/Ubuntu/CentOS/Fedora
# fi
#------INSTALL OTHER SOFTWARE------
#MAFFT
if ! [ -x "$(command -v mafft)" ]; then
echo -e "Installing 'mafft'"
wget https://mafft.cbrc.jp/alignment/software/mafft-7.487-without-extensions-src.tgz &> mafft_install.log
#wget http://mafft.cbrc.jp/alignment/software/mafft-7.305-without-extensions-src.tgz &> mafft_install.log
if [ -f mafft-7.487-without-extensions-src.tgz ]; then
tar -xvf mafft-7.487-without-extensions-src.tgz 1>/dev/null
rm mafft-7.487-without-extensions-src.tgz
cd mafft-7.487-without-extensions/core
make &>> ../../mafft_install.log
make install &>> ../../mafft_install.log
cd ../..
fi
fi
#GNU parallel
if ! [ -x "$(command -v parallel)" ]; then
echo -e "Installing 'GNU parallel'"
wget http://ftp.gnu.org/gnu/parallel/parallel-latest.tar.bz2 &> GNUparallel_install.log
if [ -f parallel-latest.tar.bz2 ]; then
tar xjvf parallel-latest.tar.bz2 1>/dev/null
rm parallel-latest.tar.bz2
cd parallel*
./configure &>> ../GNUparallel_install.log
make &>> ../GNUparallel_install.log
make install &>> ../GNUparallel_install.log
cd ..
fi
fi
#SAMtools
if ! [ -x "$(command -v samtools)" ]; then
echo -e "Installing 'samtools'"
wget https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2 &> samtools_install.log
if [ -f samtools-1.8.tar.bz2 ]; then
tar xjvf samtools-1.8.tar.bz2 1>/dev/null
rm samtools-1.8.tar.bz2
cd samtools-1.8
autoheader &>> ../samtools_install.log
autoconf -Wno-syntax &>> ../samtools_install.log
./configure --without-curses &>> ../samtools_install.log
make all all-htslib &>> ../samtools_install.log
make install all-htslib &>> ../samtools_install.log
cd ..
fi
fi
# if ! [ -x "$(command -v samtools)" ]; then
# echo -e "Installing 'samtools'"
# wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 &> samtools_install.log
# tar xjvf samtools-1.3.1.tar.bz2 1>/dev/null
# rm samtools-1.3.1.tar.bz2
# cd samtools-1.3.1
# ./configure --without-curses &>> ../samtools_install.log
# make &>> ../samtools_install.log
# make install &>> ../samtools_install.log
# cd ..
# fi
#BCFtools
if ! [ -x "$(command -v bcftools)" ]; then
echo -e "Installing 'bcftools'"
wget https://github.com/samtools/bcftools/releases/download/1.8/bcftools-1.8.tar.bz2 &> bcftools_install.log
if [ -f bcftools-1.8.tar.bz2 ]; then
tar xjvf bcftools-1.8.tar.bz2 1>/dev/null
rm bcftools-1.8.tar.bz2
cd bcftools-1.8
./configure --without-curses &>> ../bcftools_install.log
make all all-htslib &>> ../bcftools_install.log
make install all-htslib &>> ../bcftools_install.log
cd ..
fi
fi
#FastTree
if ! [ -x "$(command -v FastTree)" ]; then
echo -e "Installing 'FastTree'"
mkdir FastTree
cd FastTree
wget http://www.microbesonline.org/fasttree/FastTree &> ../fasttree_install.log
if [ -f FastTree ]; then
chmod +x FastTree
cp FastTree /usr/local/bin
wget http://www.microbesonline.org/fasttree/FastTree.c &>> ../fasttree_install.log
if [ -f FastTree.c ]; then
gcc -DOPENMP -fopenmp -O3 -finline-functions -funroll-loops -Wall -o FastTreeMP FastTree.c -lm &>> ../fasttree_install.log
chmod +x FastTreeMP
cp FastTreeMP /usr/local/bin
fi
fi
cd ..
fi
#EMBOSS
if ! [ -x "$(command -v transeq)" ]; then
echo -e "Installing 'EMBOSS'"
wget ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz &> EMBOSS_install.log
if [ -f emboss-latest.tar.gz ]; then
tar xfz emboss-latest.tar.gz 1>/dev/null
rm emboss-latest.tar.gz
cd EMBOSS-*
./configure --without-x &>> ../EMBOSS_install.log
make &>> ../EMBOSS_install.log
ldconfig &>> ../EMBOSS_install.log
make install &>> ../EMBOSS_install.log
ldconfig &>> ../EMBOSS_install.log
make install &>> ../EMBOSS_install.log
cd ..
fi
fi
#RAxML
git clone https://github.com/stamatak/standard-RAxML &> raxml_install.log
cd standard-RAxML
if ! [ -x "$(command -v raxmlHPC)" ]; then
echo -e "Installing 'raxmlHPC'"
make -f Makefile.gcc &>> ../raxml_install.log
rm *.o
fi
if [[ `grep sse3 /proc/cpuinfo` ]]; then
if ! [ -x "$(command -v raxmlHPC-SSE3)" ]; then
echo -e "Installing 'raxmlHPC-SSE3'"
make -f Makefile.SSE3.gcc &>> ../raxml_install.log
rm *.o
fi
fi
if [[ `grep avx /proc/cpuinfo` ]]; then
if ! [ -x "$(command -v raxmlHPC-AVX)" ]; then
echo -e "Installing 'raxmlHPC-AVX'"
make -f Makefile.AVX.gcc &>> ../raxml_install.log
rm *.o
fi
fi
if ! [ -x "$(command -v raxmlHPC-PTHREADS)" ]; then
echo -e "Installing 'raxmlHPC-PTHREADS'"
make -f Makefile.PTHREADS.gcc &>> ../raxml_install.log
rm *.o
fi
if [[ `grep sse3 /proc/cpuinfo` ]]; then
if ! [ -x "$(command -v raxmlHPC-PTHREADS-SSE3)" ]; then
echo -e "Installing 'raxmlHPC-PTHREADS-SSE3'"
make -f Makefile.SSE3.PTHREADS.gcc &>> ../raxml_install.log
rm *.o
fi
fi
if [[ `grep avx /proc/cpuinfo` ]]; then
if ! [ -x "$(command -v raxmlHPC-PTHREADS-AVX)" ]; then
echo -e "Installing 'raxmlHPC-PTHREADS-AVX'"
make -f Makefile.AVX.PTHREADS.gcc &>> ../raxml_install.log
rm *.o
fi
fi
cp raxmlHPC* /usr/local/bin 2>/dev/null
cd ..
#MstatX
if ! [ -x "$(command -v mstatx)" ]; then
echo -e "Installing 'MstatX'"
git clone https://github.com/gcollet/MstatX &> mstatx_install.log
cd MstatX
make &>> ../mstatx_install.log
cp mstatx /usr/local/bin
cd ..
fi
#TrimAl
if ! [ -x "$(command -v trimal)" ]; then
echo -e "Installing 'TrimAl'"
git clone https://github.com/scapella/trimal &> trimal_install.log
cd trimal/source
make &>> ../../trimal_install.log
cp trimal /usr/local/bin
cd ../..
fi
#Newick Utilities
if ! [ -x "$(command -v nw_reroot)" ]; then
echo -e "Installing 'Newick Utilities'"
# wget http://cegg.unige.ch/pub/newick-utils-1.6-Linux-x86_64-disabled-extra.tar.gz &> newickutil_install.log
# tar xfz newick-utils-1.6-Linux-x86_64-disabled-extra.tar.gz 1>/dev/null
# rm newick-utils-1.6-Linux-x86_64-disabled-extra.tar.gz
# cp newick-utils-1.6/src/nw_* /usr/local/bin
if ! [ -x "$(command -v bison)" ]; then
$installer install -y bison &> bison_install.log
fi
if ! [ -x "$(command -v flex)" ]; then
$installer install -y flex &> flex_install.log
fi
if ! [ -x "$(command -v autoreconf)" ]; then
$installer install -y dh-autoreconf &> autoreconf_install.log
fi
# from source (not working with GCC 11)
# git clone https://github.com/tjunier/newick_utils &> newickutil_install.log
# cd newick_utils/ &>> newickutil_install.log
# libtoolize &>> newickutil_install.log
# aclocal &>> newickutil_install.log
# autoheader &>> newickutil_install.log
# autoreconf -fi &>> newickutil_install.log
# ./configure &>> newickutil_install.log
# make &>> newickutil_install.log
# make check &>> newickutil_install.log
# make install &>> newickutil_install.log
# ldconfig &>> newickutil_install.log
# cd ..
#from file stored at anaconda repo
wget https://anaconda.org/bioconda/newick_utils/1.6/download/linux-64/newick_utils-1.6-h779adbc_4.tar.bz2 &> newickutil_install.log
tar -xf newick_utils-1.6-h779adbc_4.tar.bz2 &>> newickutil_install.log
cp bin/nw_* /usr/local/bin
cp lib/libnw* /usr/local/lib
fi
#bam2fastq
if ! [ -x "$(command -v bam2fastq)" ]; then
echo -e "Installing 'bam2fastq'"
wget --no-check-certificate https://gsl.hudsonalpha.org/static/software/bam2fastq-1.1.0.tgz &> bam2fastq_install.log
if [ -f bam2fastq-1.1.0.tgz ]; then
tar xfz bam2fastq-1.1.0.tgz 1>/dev/null
rm bam2fastq-1.1.0.tgz
cd bam2fastq-1.1.0
make &>> ../bam2fastq_install.log
cp bam2fastq /usr/local/bin
cd ..
fi
fi
#BLAT
#see, e.g., http://nix-bio.blogspot.cz/2013/10/installing-blat-and-blast.html for installing tips
if ! [ -x "$(command -v blat)" ]; then
echo -e "Installing 'BLAT'"
wget --no-check-certificate https://users.soe.ucsc.edu/~kent/src/blatSrc35.zip &> blat_install.log
if [ -f blatSrc35.zip ]; then
unzip blatSrc35.zip 1>/dev/null
rm blatSrc35.zip
cd blatSrc
#echo $MACHTYPE #if you get x86_64-pc-linux-gnu continue with next line, if something else write appropriate short name
MACHTYPE=x86_64
export MACHTYPE
mkdir -p lib/$MACHTYPE
mkdir -p ~/bin/$MACHTYPE
make &>> ../blat_install.log
cp ~/bin/$MACHTYPE/blat /usr/local/bin
cd ..
fi
fi
#FastUniq
if ! [ -x "$(command -v fastuniq)" ]; then
echo -e "Installing 'FastUniq'"
wget https://sourceforge.net/projects/fastuniq/files/FastUniq-1.1.tar.gz &> fastuniq_install.log
if [ -f FastUniq-1.1.tar.gz ]; then
tar xfz FastUniq-1.1.tar.gz 1>/dev/null
rm FastUniq-1.1.tar.gz
cd FastUniq/source
make &>> ../fastuniq_install.log
cp fastuniq /usr/local/bin
cd ../..
fi
fi
#Bowtie2
if ! [ -x "$(command -v bowtie2)" ]; then
echo -e "Installing 'Bowtie2'"
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.4/bowtie2-2.4.4-source.zip &> bowtie2_install.log
if [ -f bowtie2-2.4.4-source.zip ]; then
unzip bowtie2-2.4.4-source.zip 1>/dev/null
rm bowtie2-2.4.4-source.zip
cd bowtie2-2.4.4
make &>> ../bowtie2_install.log
make install &>> ../bowtie2_install.log
#cp bowtie2* /usr/local/bin
cd ..
fi
fi
#bwa
if ! [ -x "$(command -v bwa)" ]; then
echo -e "Installing 'bwa'"
git clone https://github.com/lh3/bwa.git &> bwa_install.log
#wget https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.16a.tar.bz2 &> bwa_install.log
# if [ -f bwa-0.7.16a.tar.bz2 ]; then
# tar jxf bwa-0.7.16a.tar.bz2 1>/dev/null
# rm bwa-0.7.16a.tar.bz2
# cd bwa-0.7.16a
# make &>> ../bwa_install.log
# cp bwa /usr/local/bin
# cd ..
# fi
cd bwa
make &>> ../bwa_install.log
cp bwa /usr/local/bin
cd ..
fi
#ococo (necessary for majority rule consensus building from mapped reads in BAM file)
#see https://github.com/karel-brinda/ococo
if ! [ -x "$(command -v ococo)" ]; then
echo -e "Installing 'OCOCO'"
git clone --recursive https://github.com/karel-brinda/ococo &>> ococo_install.log
cd ococo
make -j &>> ../ococo_install.log
make install &>> ../ococo_install.log
cd ..
fi
#BUCKy
if ! [ -x "$(command -v bucky)" ]; then
echo -e "Installing 'BUCKy'"
# from source (nor working with GCC 11?)
# wget http://dstats.net/download/http://www.stat.wisc.edu/~ane/bucky/v1.4/bucky-1.4.4.tgz &> bucky_install.log
# if [ -f bucky-1.4.4.tgz ]; then
# tar -xzvf bucky-1.4.4.tgz 1>/dev/null
# rm bucky-1.4.4.tgz
# cd bucky-1.4.4/src/
# make &>> ../../bucky_install.log
# cp mbsum /usr/local/bin
# cp bucky /usr/local/bin
# cd ../..
# fi
# from binary file stored in enaconda repo
wget https://anaconda.org/ipyrad/bucky/v1.4.3/download/linux-64/bucky-v1.4.3-0.tar.bz2 &> bucky_install.log
if [ -f bucky-v1.4.3-0.tar.bz2 ]; then
tar -xf bucky-v1.4.3-0.tar.bz2 1>/dev/null
rm bucky-v1.4.3-0.tar.bz2
cp bin/mbsum /usr/local/bin
cp bin/bucky /usr/local/bin
fi
fi
#seqtk
if ! [ -x "$(command -v seqtk)" ]; then
echo -e "Installing 'seqtk'"
git clone https://github.com/lh3/seqtk.git &>> seqtk_install.log
cd seqtk
make &>> ../seqtk_install.log
make install &>> ../seqtk_install.log
cd ..
fi
#p4 (only necessary for combining bootstrap support in Astral and Astrid trees)
#see http://p4.nhm.ac.uk/installation.html
#now with python3
#For compilation on Fedora/CentOS/OpenSUSE you need to specify where 'gsl' is installed (in setup.py) - modification of 'setup.py' is included below
if ! [ -x "$(command -v p4)" ]; then
echo -e "Installing 'p4'"
if [[ $distribution =~ "Debian" ]]; then
if ! [[ `pip3 --disable-pip-version-check show numpy 2>/dev/null | grep Version` ]]; then
pip3 install numpy &> numpy_install.log
#$installer install -y python-numpy &> numpy_install.log #Debian/Ubuntu/OpenSUSE
fi
if ! [[ `pip3 --disable-pip-version-check show scipy 2>/dev/null | grep Version` ]]; then
pip3 install scipy &> scipy_install.log
$installer install -y python-scipy &> scipy_install.log #Debian, OpenSUSE
fi
elif [[ $distribution =~ "OpenSUSE" ]]; then
if ! [[ `pip3 --disable-pip-version-check show numpy 2>/dev/null | grep Version` ]]; then
#pip3 install numpy &> numpy_install.log
$installer install -y python-numpy-devel &> numpy_install.log #Debian/Ubuntu/OpenSUSE
fi
if ! [[ `pip3 --disable-pip-version-check show scipy 2>/dev/null | grep Version` ]]; then
pip3 install scipy &> scipy_install.log
#$installer install -y python-scipy &> scipy_install.log #Debian, OpenSUSE
fi
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
if ! [[ `pip3 --disable-pip-version-check show numpy 2>/dev/null | grep Version` ]]; then
#pip3 install numpy &> numpy_install.log
$installer install -y python3-numpy &> numpy_install.log #CentOS, Fedora
fi
if ! [[ `pip3 --disable-pip-version-check show scipy 2>/dev/null | grep Version` ]]; then
#pip3 install scipy &> scipy_install.log
$installer install -y python3-scipy &> scipy_install.log #CentOS, Fedora
fi
fi
if [[ $distribution =~ "Debian" ]]; then
$installer install -y libgsl0-dev &> libgsl_install.log #Debian
$installer install -y python-dev &> python-dev_install.log #Debian
$installer install -y python-setuptools &> python-setuptools_install.log
elif [[ $distribution =~ "OpenSUSE" ]] || [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
$installer install -y gsl-devel &> libgsl_install.log #CentOS, Fedora and OpenSUSE
$installer install -y python-devel &> python-dev_install.log #CentOS, Fedora and OpenSUSE
$installer install -y python-setuptools &> python-setuptools_install.log
fi
if [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
$installer install redhat-rpm-config &> rpm-config_install.log
fi
#install python modules 'future' and 'bitarray'
if [[ $distribution =~ "Debian" ]]; then
if ! [[ `pip3 --disable-pip-version-check show future 2>/dev/null | grep Version` ]]; then
pip3 install future &> python-future_install.log
fi
if ! [[ `pip3 --disable-pip-version-check show bitarray 2>/dev/null | grep Version` ]]; then
pip3 install bitarray &> python-bitarray_install.log
fi
else
if ! [[ `pip3 --disable-pip-version-check show future 2>/dev/null | grep Version` ]]; then
pip3 install future &> python-future_install.log
fi
if ! [[ `pip3 --disable-pip-version-check show bitarray 2>/dev/null | grep Version` ]]; then
pip3 install bitarray &> python-bitarray_install.log
fi
fi
#install NLopt
if [[ $distribution =~ "Debian" ]]; then
$installer install -y libnlopt-dev &> libnlopt_install.log
elif [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
$installer install -y NLopt-devel &> libnlopt_install.log
elif [[ $distribution =~ "OpenSUSE" ]]; then
$installer install -y nlopt-devel &> libnlopt_install.log
fi
git clone https://github.com/pgfoster/p4-phylogenetics &> p4_install.log
cd p4-phylogenetics
#Modify setup.py to be able to find gsl
if [[ $distribution =~ "OpenSUSE" ]] || [[ $distribution =~ "CentOS" ]] || [[ $distribution =~ "Fedora" ]]; then
replace="my_include_dirs = [\'\/usr\/include\/\']"
#sed -i.bak "46s/.*/$replace/" setup.py
#sed -i.bak2 "47s/# //" setup.py
fi
python3 setup.py build &>> ../p4_install.log
python3 setup.py install &>> ../p4_install.log
#python2 setup.py build_ext -i &>> ../p4_install.log
chmod +x make_pf.sh
./make_pf.sh &>> ../p4_install.log
cd ..
fi
#kindel (necessary for majority rule consensus building from mapped reads in BAM file)
#requires v0.1.4 (higher version will not work as they are missing option for threshold!)
#see https://pypi.python.org/pypi/kindel
if ! [ -x "$(command -v kindel)" ]; then
echo -e "Installing 'kindel'"
# if [[ $distribution =~ "Debian" ]]; then
# $installer install -y python3-dev &> python3-dev_install.log #Debian
# elif [[ $distribution =~ "OpenSUSE" ]] || [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
# $installer install -y python3-devel &> python3-dev_install.log #CentOS, Fedora and OpenSUSE
# fi
if [[ $distribution =~ "Fedora" ]]; then
python3 -m pip install 'kindel==0.1.4' &>> kindel_install.log
else
pip3 install 'kindel==0.1.4' &>> kindel_install.log
fi
fi
#VCFtools
if ! [ -x "$(command -v vcftools)" ]; then
echo -e "Installing 'VCFtools'"
git clone https://github.com/vcftools/vcftools &>> vcftools_install.log
cd vcftools
./autogen.sh &>> ../vcftools_install.log
./configure &>> ../vcftools_install.log
make &>> ../vcftools_install.log
make install &>> ../vcftools_install.log
cd ..
fi
#Ruby
if ! [ -x "$(command -v ruby)" ]; then
echo -e "Installing 'ruby'"
if [[ $distribution =~ "Debian" ]]; then
$installer install -y ruby-full &> ruby_install.log
else
$installer install -y ruby &> ruby_install.log
fi
fi
#other python3 modules (mainly for Dsuite and phyparts)
if ! [[ `pip3 --disable-pip-version-check show pandas 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'pandas for python3'"
pip3 install pandas &> python3-pandas_install.log
fi
if ! [[ `pip3 --disable-pip-version-check show matplotlib 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'matplotlib for python3'"
pip3 install matplotlib &> python3-matplotlib_install.log
fi
if ! [[ `pip3 --disable-pip-version-check show cairosvg 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'cairosvg for python3'"
pip3 install cairosvg &> python3-cairosvg_install.log
fi
if ! [[ `pip3 --disable-pip-version-check show PyQt5 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'PyQt5 for python3'"
#older version installed, newer version makes problems with installation (missing dependencies?)
pip3 install PyQt5==5.13.2 &> python3-PyQt5_install.log
fi
if ! [[ `pip3 --disable-pip-version-check show ete3 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'ete3 for python3'"
pip3 install ete3 &> python3-ete3_install.log
fi
#other python2 modules (for PartitionFinder)
if [[ $distribution =~ "Debian" ]]; then
if ! [[ `pip2 --disable-pip-version-check show pandas 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'pandas for python2'"
pip2 install pandas &> python-pandas_install.log
#$installer install -y python-pandas &> python-pandas_install.log #Debian
fi
if ! [[ `pip2 --disable-pip-version-check show scikit-learn 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'scikit-learn for python2'"
pip2 install scikit-learn &> python-sklearn_install.log
#$installer install -y python-sklearn &> python-sklearn_install.log #Debian
fi
if ! [[ `pip2 --disable-pip-version-check show tables 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'tables for python2'"
pip2 install tables &> python-tables.log
fi
if ! [[ `pip2 --disable-pip-version-check show parsing 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'parsing for python2'"
pip2 install parsing &> python-parsing.log
fi
if ! [[ `pip2 --disable-pip-version-check show pyparsing 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'pyparsing for python2'"
pip2 install pyparsing &> python-pyparsing.log
fi
elif [[ $distribution =~ "OpenSUSE" ]] || [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
if ! [[ `pip2.7 --disable-pip-version-check show pandas 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'pandas for python2'"
pip2.7 install pandas &> python-pandas_install.log #CentOS, Fedora and OpenSUSE
fi
if ! [[ `pip2.7 --disable-pip-version-check show scikit-learn 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'scikit-learn for python2'"
pip2.7 install scikit-learn &> python-sklearn_install.log #CentOS, Fedora and OpenSUSE
fi
if ! [[ `pip2.7 --disable-pip-version-check show tables 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'tables for python2'"
pip2.7 install tables &> python-tables.log
fi
if ! [[ `pip2.7 --disable-pip-version-check show parsing 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'parsing for python2'"
pip2.7 install parsing &> python-parsing.log
fi
if ! [[ `pip2.7 --disable-pip-version-check show pyparsing 2>/dev/null | grep Version` ]]; then
echo -e "Installing 'pyparsing for python2'"
pip2.7 install pyparsing &> python-pyparsing.log
fi
fi
#OpenMPI
if [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
module load mpi/openmpi-x86_64 2>/dev/null
if ! [ -x "$(command -v mpicc)" ]; then
echo -e "\nDo you want to install ExaML [y/n]:"
read -s -n 1 instexaml
if [[ $instexaml =~ "y" ]]; then
echo -e "Installing 'OpenMPI'"
$installer -y install openmpi openmpi-devel &> openmpi_install.log
$installer -y install environment-modules &>> openmpi_install.log
echo -e "\nPlease logout and login back and run again 'install_software.sh' in order to complete ExaML installation" && exit 3
fi
else
instexaml=yes
fi
else
if ! [ -x "$(command -v mpicc)" ]; then
echo -e "Installing 'OpenMPI'"
if [[ $distribution =~ "Debian" ]]; then
instexaml=yes
$installer -y install mpi-default-dev &> openmpi_install.log
elif [[ $distribution =~ "OpenSUSE" ]]; then
instexaml=yes
wget https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.gz &> openmpi_install.log
tar -xvf openmpi-2.1.1.tar.gz 1>/dev/null
cd openmpi-2.1.1/
./configure &>> openmpi_install.log
make &>> openmpi_install.log
make install &>> openmpi_install.log
ldconfig &>> openmpi_install.log
cd ..
fi
fi
fi
#ExaML
if [[ $instexaml =~ "y" ]]; then
if ! [ -x "$(command -v examl)" ]; then
echo -e "Installing 'ExaML'"
if [[ $distribution =~ "Fedora" ]] || [[ $distribution =~ "CentOS" ]]; then
module load mpi/openmpi-x86_64
fi
git clone https://github.com/stamatak/ExaML &> examl_install.log
cd ExaML/parser
make -f Makefile.SSE3.gcc &> ../../examl_install.log
cp parse-examl /usr/local/bin
cd ../examl
make -f Makefile.SSE3.gcc &> ../../examl_install.log
cp examl /usr/local/bin
if [[ `grep avx /proc/cpuinfo` ]]; then
make -f Makefile.AVX.gcc &> ../../examl_install.log
cp examl-AVX /usr/local/bin
fi
cd ../..
fi
fi
#Dsuite
if ! [ -x "$(command -v Dsuite)" ]; then
echo -e "Installing 'Dsuite'"
git clone https://github.com/millanek/Dsuite.git &>> Dsuite_install.log
cd Dsuite
#Modify Dsuite_utils.cpp for smooth compiling under newer gcc