masimrs/singularity at master · MASILab/masimrs · GitHub

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Bootstrap: docker
From: ubuntu:18.04

%post -c /bin/bash

    cd /

    # Update all libraries
    apt-get -y update

    # Install xvfb
    apt-get -y install xvfb

    # Install ghostscript for pdf management
    apt-get -y install ghostscript

    # Install MRTrix3
    apt-get -y install git g++ python python-numpy libeigen3-dev zlib1g-dev libqt4-opengl-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev python3-distutils
    git clone https://github.com/MRtrix3/mrtrix3.git
    cd mrtrix3
    git checkout 3.0.3
    ./configure
    ./build
    cd /

    # Install LCModel (Without GUI Capabilites) and Basis Sets
    apt-get -y install wget unzip
    mkdir -p lcmodel
    cd lcmodel
    wget http://s-provencher.com/pub/LCModel/programs/lcm-64.tar
    tar xf lcm-64.tar
    rm lcm-64.tar
    gunzip -c lcm-core.tar.gz | tar xf -
    rm lcm-core.tar.gz
    wget http://s-provencher.com/pub/LCModel/3t.zip
    unzip 3t.zip
    mv 3t/ basis-sets-3t/
    cd /

    # Make custom folders
    mkdir -p /INPUTS
    mkdir -p /OUTPUTS

    # Set Permissions
    chmod 755 /INPUTS
    chmod 755 /OUTPUTS

    # Install source code
    apt-get -y install git gcc libpq-dev python3.8 python3.8-dev python3.8-venv python3-pip python3-wheel python3-numpy
    git clone https://github.com/MASILab/masimrs.git
    cd masimrs
    python3.8 -m venv venv
    source venv/bin/activate
    pip3.8 install wheel
    pip3.8 install --upgrade pip setuptools wheel
    pip3.8 install -r requirements.txt
    deactivate
    cd /

%environment

    # MRTrix3
    export PATH="/mrtrix3/bin:$PATH"

    # LCModel
    export PATH="/lcmodel/.lcmodel/bin:$PATH"

%runscript

    xvfb-run -a --server-num=$((65536+$$)) --server-args="-screen 0 1600x1280x24 -ac" bash /masimrs/run_masimrs.sh "$@"