Singularity_elikopy

Bootstrap: docker
From: nvidia/cuda:9.1-devel-centos7

%post -c /bin/bash
    cd /

    # Prepare directories for installing applications
    mkdir -p Software
    mkdir -p Installer_tmp

    # Update all libraries
    yum -y update
    yum install epel-release -y
    
    # Install X11 + some utils
    yum install -y xorg-x11-server-Xorg xorg-x11-xauth xorg-x11-apps nano
    yum groupinstall "Development Tools"
    
    # Requirements FreeSurfer
    yum update -y
    yum install git wget tcsh gcc gcc-c++ libgfortran-static make vim-common ca-certificates -y
    yum install lapack-devel lapack-static blas-devel blas-static zlib-devel -y 
    yum install python-devel python3-devel -y
    yum install libX11-devel libXmu-devel mesa-libGL-devel -y
    
    # Requirements FSL
    yum install expat-devel libX11-devel mesa-libGL-devel zlib-devel libpng-devel -y
    
    # Requirements MRTrix3
    yum install git gcc-g++ python eigen3-devel zlib-devel mesa-libGL-devel fftw-devel libtiff-devel -y
    python3 -m pip install numpy
    yum install centos-release-scl -y
    yum install devtoolset-8 -y
    scl enable devtoolset-8 bash
    
    #Requirements Convert3D
    yum -y install wget tar
    
    #Requirements ANTs
    yum -y install git gcc-c++ zlib-devel cmake cmake3
    
    alternatives --install /usr/local/bin/cmake cmake /usr/bin/cmake 10 \
    --slave /usr/local/bin/ctest ctest /usr/bin/ctest \
    --slave /usr/local/bin/cpack cpack /usr/bin/cpack \
    --slave /usr/local/bin/ccmake ccmake /usr/bin/ccmake \
    --family cmake
    
    alternatives --install /usr/local/bin/cmake cmake /usr/bin/cmake3 20 \
    --slave /usr/local/bin/ctest ctest /usr/bin/ctest3 \
    --slave /usr/local/bin/cpack cpack /usr/bin/cpack3 \
    --slave /usr/local/bin/ccmake ccmake /usr/bin/ccmake3 \
    --family cmake
        
    # Install MRTrix3
    cd /Software
    git clone https://github.com/MRtrix3/mrtrix3.git
    cd mrtrix3
    git checkout 3.0.3
    ./configure -nogui -openmp 
    ./build
    cd /

    # Install FSL
    wget -O /Installer_tmp/fslinstaller.py "https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py"
    cd /Installer_tmp
    export LC_ALL="en_US.UTF-8"
    python fslinstaller.py -d /Software/fsl6 -V 6.0.4
    cd /

    # Install Convert3D (stable build 1.0.0)
    wget -O /Installer_tmp/c3d-1.0.0-Linux-x86_64.tar.gz "https://downloads.sourceforge.net/project/c3d/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fc3d%2Ffiles%2Fc3d%2F1.0.0%2Fc3d-1.0.0-Linux-x86_64.tar.gz%2Fdownload&ts=1571934949"
    tar -xf /Installer_tmp/c3d-1.0.0-Linux-x86_64.tar.gz -C /Software/
    cd /

    # Clean up
    rm -r /Installer_tmp/c3d-1.0.0-Linux-x86_64.tar.gz  
    
    # Install ANTs
    cd /Installer_tmp
    mkdir ants_installer
    cd ants_installer
    git clone https://github.com/stnava/ANTs.git
    cd ANTs
    git checkout v2.3.5
    cd .. 
    mkdir ants_build
    cd ants_build
    cmake3 /Installer_tmp/ants_installer/ANTs -DCMAKE_INSTALL_PREFIX=/Software/ants
    make 2>&1 | tee build.log
    make 2>&1 | tee build.log
    cd ANTS-build
    make install 2>&1 | tee install.log
    cd /
    
    # Clean up
    rm -r /Installer_tmp/ants_installer/

    # Install FreeSurfer
    yum -y install bc binutils libgomp1 perl psmisc sudo tar tcsh unzip uuid-dev vim-common libjpeg62-dev
    wget -O /Installer_tmp/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz "https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz"
    tar -C /Software -xzvf /Installer_tmp/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz
    echo "This is a dummy license file. Please bind your freesurfer license file to this file." > /Software/freesurfer/license.txt
    cd /
    
    # Clean up
    rm -r /Installer_tmp/freesurfer-linux-centos7_x86_64-7.1.1.tar.gz
    
    # Make custom folders
    mkdir -p PROJECTS

    # Set Permissions
    chmod 755 /PROJECTS
    chmod 755 /Software
    
    # Install MF 
    yum -y install git gcc libpq-dev python-dev python-pip python3 python3-dev python3-pip python3-venv python3-wheel
    cd /Software
    git clone https://github.com/rensonnetg/microstructure_fingerprinting.git
    cd microstructure_fingerprinting
    python3 setup.py install
    cd /

    # Install ElikoPy
    cd /Software
    git clone https://github.com/Hyedryn/elikopy
    cd elikopy
    python3 -m pip install -r requirements.txt
    python3 setup.py install
    cd /

    # Clean up
    rm -r /Installer_tmp

%environment
    # MRTrix3
    export PATH="/Software/mrtrix3/bin:$PATH"
    # FSL
    FSLDIR=/Software/fsl6
    . ${FSLDIR}/etc/fslconf/fsl.sh
    PATH=${FSLDIR}/bin:${PATH}
    export FSLDIR PATH
    # Convert3D
    export PATH="/Software/c3d-1.0.0-Linux-x86_64/bin:$PATH"
    # ANTs
    export ANTSPATH=/Software/ants/bin/
    export PATH=${ANTSPATH}:$PATH
    # FreeSurfer
    export FREESURFER_HOME=/Software/freesurfer
    source $FREESURFER_HOME/SetUpFreeSurfer.sh

%runscript
    xvfb-run -a --server-num=$((65536+$$)) --server-args="-screen 0 1600x1280x24 -ac" bash /Software/elikopy/run_elikopy.sh /PROJECTS "$@"