easy_gate.sh

#!/bin/sh

# Easy GATE Installation 
# Simplify the Installation of the GATE monte-carlo simulation toolkit
# Version 1.2
# Created on: Nov 25, 2018
# Updated on: April 06, 2020
# Author: Alexandre CARRE (alexandre.carre@gustaveroussy.fr)
# NB : Use this script at your own Risk

echo "       *     ,MMM8&&&.            *       "
echo "            MMMM88&&&&&    .              "
echo "           MMMM88&&&&&&&                  "
echo "  *        M Easy GATE &          *       "
echo "           MMM V1.3 &&&&                  "
echo "           'MMM88&&&&&&'             .    "
echo "             'MMM8&&&'      *             "
echo "    |\___/|                               "
echo "    )     (           installation :      "
echo "   =\     /=      - Package Requirements  "
echo "     )===(        - ROOT 6.20/04          "
echo "    /     \       - Geant4 10.6.p01       "
echo "    |     |       - InsightToolkit 5.0.1  "
echo "   /       \      - Gate V9.0             "
echo "   \       /      - Cluster tools (opt)   "
echo "  _/\__  _/_/\_/\_/\_/\_/\_/\_/\_/\_/\_/\ "
echo "  |  |( (  |  |Author : Alexandre CARRE  |"  
echo "  |  | ) ) |  |  |  |  |  |  |  |  |  |  |"
echo "  |  |(_(alexandre.carre@gustaveroussy.fr|"
echo " "


# simple function to check http response code before downloading a remote file
# example usage:
# if `validate_url $url >/dev/null`; then dosomething; else echo "does not exist"; fi
# https://gist.github.com/hrwgc/7455343
function validate_url(){
  if [[ `wget -S --spider $1  2>&1 | grep 'HTTP/1.1 200 OK'` ]]; then echo "true"; fi
}

## Check os release
DISTRO=$( cat /etc/*-release | tr [:upper:] [:lower:] | grep -Poi '(debian|ubuntu|red hat|centos|scientific|opensuse)' | uniq -c | sort -r | head -1|  xargs | cut -d" " -f2- )
if [[ -z $DISTRO ]]; then
    DISTRO='unknown'
    echo "Detected Linux distribution: $DISTRO"
    echo "The script has not been done for your distribution, sorry ..."
    return
else
    echo "Detected Linux distribution: $DISTRO"
fi

if [[ $DISTRO =~ "debian" ]] || [[ $DISTRO =~ "ubuntu" ]]; then
    INSTALL_TYPE='apt'
elif [[ $DISTRO =~ "red hat" ]] || [[ $DISTRO =~ "centos" ]] || [[ $DISTRO =~ "scientific" ]]; then
    INSTALL_TYPE='yum'
elif [[ $DISTRO =~ "opensuse" ]]; then
    INSTALL_TYPE='zypper'
fi

## Check internet connection
wget -q --spider http://google.com
if [ $? -eq 0 ]; then
    echo "Your internet connection has been successfully tested"
else
    echo "Please check your internet connection & restart the script"
    return
fi

## Installation of GATE or not ?
while true; do
    read -p "Do you wish to install GATE and its dependencies [y/n]?" yn
    case $yn in
        [Yy]* ) break;;
        [Nn]* ) return;;
        * ) echo "Please answer yes or no.";;
    esac
done

## Installation of GATE require sudo password
if [[ "$EUID" = 0 ]]; then
    echo "You are logged as root"
    echo "The installation can't be processed as root"
    return
else
    sudo -k # make sure to ask for password on next sudo
    if sudo true; then
        echo "correct password"
    else
        echo "wrong password"
    return
    fi
fi

# keep sudo alive
while true; do
  sleep 200
  sudo -n true
  kill -0 "$$" 2>/dev/null || exit
done &

## Verify if there is a version of GATE already installed ?
if which Gate 2>/dev/null
    then
        echo "'Gate' seems to be already installed."
            while true; do
            read -p "Are you sure you want to proceed with the installation [y/n]?" yn
            case $yn in
            [Yy]* ) break;;
            [Nn]* ) return;;
            * ) echo "Please answer yes or no.";;
        esac
   done
fi

## Personalize the GATE installation path.
while true; do
    read -p "Do you want to personalize the installation path [y/n]? (default : usr/local)" yn
    case $yn in
        [Yy]* ) read -p "Enter path: " GPTH
    if [ -d "$GPTH" ]
    then
            echo "$GPTH is valide."
        break
    else
            echo "$GPTH is not valide. Please check the path enter !"
    fi;;
        [Nn]* ) GPTH='/usr/local'; break;;
        * ) echo "Please answer yes or no.";;
    esac
done

## Check free space on Disk (require 13 GBs)
FREE=`df -k --output=avail "$PWD" $GPTH | tail -n1`   # df -k not df -h
if [[ $FREE -lt 13631488 ]]; then               # 13G = 13*1024*1024k
     echo "You need at least 13 GBs of free space to install GATE !"
     echo "less than 13 GBs free in your installation path!"
     return
fi

## Go to the installation directory
cd $GPTH
sudo mkdir GATE
sudo chmod -R 777 GATE
cd $GPTH/GATE

## Download all the files for Gate installation
#root
url_root="https://root.cern.ch/download/root_v6.20.04.source.tar.gz"
if validate_url url_root; then
    echo "Url : $url_root exists..."
    wget https://root.cern.ch/download/root_v6.20.04.source.tar.gz
    tar -xvzf root_v6.20.04.source.tar.gz
    rm root_v6.20.04.source.tar.gz
  else
    echo "Url : $url_root doesn't exists.."
    echo "The link seems to be broken, please contact the author to update the script"
    return
fi

#itk
url_itk="https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0.1/InsightToolkit-5.0.1.tar.gz"
if validate_url url_itk; then
    echo "Url : $url_itk exists..."
    wget https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0.1/InsightToolkit-5.0.1.tar.gz
    tar -xvzf InsightToolkit-5.0.1.tar.gz
    rm InsightToolkit-5.0.1.tar.gz
else
    echo "Url : $url_itk doesn't exists.."
    echo "The link seems to be broken, please contact the author to update the script"
    return
fi
#geant4
url_geant="http://cern.ch/geant4-data/releases/geant4.10.06.p01.tar.gz"
if validate_url url_geant; then
    echo "Url : $url_geant exists..."
    wget http://cern.ch/geant4-data/releases/geant4.10.06.p01.tar.gz
    tar -xvzf geant4.10.06.p01.tar.gz
    rm geant4.10.06.p01.tar.gz
else
    echo "Url : $url_geant doesn't exists.."
    echo "The link seems to be broken, please contact the author to update the script"
    return
fi
#gate
url_gate=" https://github.com/OpenGATE/Gate/archive/v9.0.zip"
if validate_url url_gate; then
    echo "Url : $url_gate exists..."
    wget  https://github.com/OpenGATE/Gate/archive/v9.0.zip
    unzip v9.0.zip
    rm v9.0.zip
else
    echo "Url : $url_gate doesn't exists.."
    echo "The link seems to be broken, please contact the author to update the script"
    return
fi

## Installation of package requirements
echo "Installing the nice-to-have pre-requisites"
if [ "$INSTALL_TYPE" = "yum" ]; then
sudo yum check-update
# To get Required packages
sudo yum install git cmake gcc-c++ gcc binutils libX11-devel libXpm-devel libXft-devel libXext-devel -y
# To get optional packages
sudo yum install gcc-gfortran openssl-devel pcre-devel mesa-libGL-devel mesa-libGLU-devel glew-devel ftgl-devel mysql-devel fftw-devel cfitsio-devel graphviz-devel avahi-compat-libdns_sd-devel libldap-dev python-devel libxml2-devel gsl-static -y
fi

if [ "$INSTALL_TYPE" = "zypper" ]; then
sudo zypper update -y
# To get Required packages
sudo zypper --non-interactive --quiet install git bash cmake gcc-c++ gcc binutils xorg-x11-libX11-devel xorg-x11-libXpm-devel xorg-x11-devel xorg-x11-proto-devel xorg-x11-libXext-devel
# To get optional packages
sudo zypper --non-interactive --quiet install gcc-fortran libopenssl-devel pcre-devel Mesa glew-devel pkg-config libmysqlclient-devel fftw3-devel libcfitsio-devel graphviz-devel libdns_sd avahi-compat-mDNSResponder-devel openldap2-devel python-devel libxml2-devel krb5-devel gsl-devel libqt4-devel
fi

if [ "$INSTALL_TYPE" = "apt" ]; then
sudo apt-get update
# To get Required packages
sudo apt-get install git cmake build-essential libqt4-opengl-dev qt4-qmake libqt4-dev libx11-dev libxmu-dev libxpm-dev libxft-dev libtbb-dev libnet-dev -y
# To get optional packages
sudo apt-get install gfortran libssl-dev libpcre3-dev xlibmesa-glu-dev libglew1.5-dev libftgl-dev libmysqlclient-dev libfftw3-dev libcfitsio-dev graphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python-dev libxml2-dev libkrb5-dev libgsl0-dev -y
fi

echo -e "\n"
echo 'Installation of pre-requisites done.'
echo -e "\n"
## Installation of ROOT
echo "Installation of root-6.20.04"
mkdir root-6.20.04-build
cd $GPTH/GATE/root-6.20.04-build
cmake ../root-6.20.04
cmake --build . -- -j$(nproc)
source $GPTH/GATE/root-6.20.04-build/bin/thisroot.sh
cd ..
echo "Installation of root-6.20.04 done."
echo -e "\n"
## Installation of Geant4
echo "Installation of Geant4 10.6.p01"
mkdir geant4.10.06.p01-build
mkdir geant4.10.06.p01-install
cd $GPTH/GATE/geant4.10.06.p01-build
cmake -DCMAKE_INSTALL_PREFIX=$GPTH/GATE/geant4.10.06.p01-install -DCMAKE_BUILD_TYPE=RELEASE -DGEANT4_BUILD_MULTITHREADED=OFF -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_G3TOG4=OFF -DGEANT4_USE_GDML=OFF -DGEANT4_USE_INVENTOR=OFF -DGEANT4_USE_OPENGL_X11=ON -DGEANT4_USE_QT=ON -DGEANT4_USE_RAYTRACER_X11=OFF -DGEANT4_USE_SYSTEM_EXPAT=ON -DGEANT4_USE_SYSTEM_ZLIB=OFF -DGEANT4_USE_XM=OFF $GPTH/GATE/geant4.10.06.p01
make -j$(nproc)
make install
source $GPTH/GATE/geant4.10.06.p01-install/bin/geant4.sh
cd ..
echo "Installation of Geant4 10.4.p02 done."
echo -e "\n"
## Installation of ITK
echo "Installation of ITK 5.0.1 "
cd $GPTH/GATE/InsightToolkit-5.0.1
mkdir bin
cd bin
cmake DITK_USE_REVIEW=ON -DBUILD_EXAMPLES=ON -DBUILD_TESTING=ON -DINSTALL_GTEST=ON -DITKV3_COMPATIBILITY=OFF -DITK_BUILD_DEFAULT_MODULES=ON -DITK_WRAP_PYTHON=OFF ..
make -j$(nproc)
sudo make install
cd ../..
echo "Installation of ITK 5.0.1 done."
echo -e "\n"
## Installation of GATE
echo "Installation of Gate V9.0"
mkdir Gate-9.0-build
mkdir Gate-9.0-install
cd Gate-9.0-build
cmake -DCMAKE_INSTALL_PREFIX=$GPTH/GATE/Gate-9.0-install -DBUILD_TESTING=OFF -DCMAKE_BUILD_TYPE=RELEASE -DGATE_DOWNLOAD_BENCHMARKS_DATA=OFF -DGATE_USE_DAVIS=OFF -DGATE_USE_ECAT7=OFF -DGATE_USE_GEANT4_UIVIS=ON -DGATE_USE_GPU=OFF -DGATE_USE_ITK=ON -DGATE_USE_LMF=OFF -DGATE_USE_OPTICAL=ON -DGATE_USE_RTK=OFF -DGATE_USE_STDC11=ON -DGATE_USE_SYSTEM_CLHEP=OFF -DGATE_USE_XRAYLIB=OFF -DGeant4_DIR=$GPTH/GATE/geant4.10.06.p01-install/lib/Geant4-10.6.1 -DITK_DIR=/usr/local/lib/cmake/ITK-5.0 -DROOTCINT_EXECUTABLE=$GPTH/GATE/root-6.20.04-build/bin/rootcint -DROOT_CONFIG_EXECUTABLE=$GPTH/GATE/root-6.20.04-build/bin/root-config $GPTH/GATE/Gate-9.0
make -j$(nproc)
make install
echo "Installation of Gate V9.0 done."
cd ..

## Export GATE environnment (path variable)
touch gate_env.sh
echo 'source' $GPTH'/GATE/root-6.20.04-build/bin/thisroot.sh' >> gate_env.sh
echo 'source' $GPTH'/GATE/geant4.10.06.p01-install/bin/geant4.sh' >> gate_env.sh
echo 'export PATH=$PATH:'$GPTH'/GATE/Gate-9.0-install/bin' >> gate_env.sh
echo -e "\n" >> ~/.bashrc
echo '# export path variable for GATE' >> ~/.bashrc
echo 'alias gate90'='"source '$GPTH'/GATE/gate_env.sh''"' >> ~/.bashrc
source ~/.bashrc

## verify if Gate is installed and present in $GPTH/GATE/Gate-9.0-install/bin
gate90
if ! which Gate 2>/dev/null
then
    echo "'Gate' was not found in PATH, a problem seems to be appeared during installation."
    echo "Maybe check error message during installation."
    return
else
    echo "'Gate' was successfully installed"
fi

## Installation of Cluster tools or not ?
if [ "$INSTALL_TYPE" = "apt" ]; then
while true; do
    read -p "Do you wish to install the Cluster tools (HTcondor) [y/n]?
Advice if you are not an advanced user : Always answer yes for HTcondor prompt GUI  " yn
    case $yn in
        [Yy]* ) break;;
        [Nn]* ) return;;
        * ) echo "Please answer yes or no.";;
    esac
done
## Installation of Cluster tools for Ubuntu users
#jobsplitter
cd $GPTH/GATE/Gate-9.0/cluster_tools/jobsplitter
make
cp $GPTH/GATE/Gate-9.0/cluster_tools/jobsplitter/gjs $GPTH/GATE/Gate-9.0-install/bin
#filemerger
cd $GPTH/GATE/Gate-9.0/cluster_tools/filemerger
make
cp $GPTH/GATE/Gate-9.0/cluster_tools/filemerger/gjm $GPTH/GATE/Gate-9.0-install/bin
#HTcondor for multicore processing (clustering) (always anwser yes to gui prompt for easy use)
sudo apt-get install htcondor -y
sudo condor_master
if ! hash condor_status 2>/dev/null
then
    echo "'HTcondor' was not found, a problem seems to be appeared during installation."
    echo "Maybe check error message during installation."
else
    echo "HTcondor was successfully installed"
fi
fi
cd
return