Fernet/Singularity.def at master · DiCIPHR-Lab/Fernet · GitHub

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Bootstrap: localimage
From: /cbica/home/annavazs/ubuntu_20.04.sif

%labels
    Author Sai Krishna Chaitanya Annavazala
    Description FERNET with Python packages and ANTs N4BiasFieldCorrection

%files
    /cbica/home/annavazs/temp/Fernet /opt/

%environment
    export PATH=/opt/ants/bin:$PATH
    export PYTHONNOUSERSITE=1
    export LC_ALL=C.UTF-8
    export LANG=C.UTF-8
    export PYTHONPATH=/opt/Fernet:$PYTHONPATH

%post
    export DEBIAN_FRONTEND=noninteractive

    apt-get update && apt-get install -y \
        python3 \
        python3-pip \
        python3-dev \
        git \
        wget \
        unzip \
        build-essential \
        libgl1-mesa-glx \
        libglib2.0-0 \
        libgomp1

    rm -rf /var/lib/apt/lists/*

    python3 -m pip install --upgrade pip setuptools wheel

    python3 -m pip install \
        numpy \
        scipy \
        nibabel \
        pandas \
        scikit-learn \
        dipy

    mkdir -p /opt/ants
    cd /opt
    wget https://github.com/ANTsX/ANTs/releases/download/v2.6.5/ants-2.6.5-ubuntu18.04-X64-gcc.zip
    unzip ants-2.6.5-ubuntu18.04-X64-gcc.zip
    mv ants-2.6.5/bin /opt/ants/bin
    rm -rf ants-2.6.5/ ants-2.6.5-ubuntu18.04-X64-gcc.zip

    cd /opt/Fernet

%runscript
    export PYTHONPATH=/opt/Fernet:$PYTHONPATH
    cd /opt/Fernet
    OPTS=""

    while getopts "d:o:m:r:b:w:c:x:n:BG" opt; do
        case "$opt" in
            d) OPTS="$OPTS -d $OPTARG" ;;
            o) OPTS="$OPTS -o $OPTARG" ;;
            m) OPTS="$OPTS -m $OPTARG" ;;
            r) OPTS="$OPTS -r $OPTARG" ;;
            b) OPTS="$OPTS -b $OPTARG" ;;
            w) OPTS="$OPTS -w $OPTARG" ;;
            c) OPTS="$OPTS -c $OPTARG" ;;
            x) OPTS="$OPTS -x $OPTARG" ;;
            n) OPTS="$OPTS -n $OPTARG" ;;
            B) OPTS="$OPTS -B" ;;
            G) OPTS="$OPTS -G" ;;
            *) echo "Invalid option: -$OPTARG" >&2; exit 1 ;;
        esac
    done

    exec python3 /opt/Fernet/scripts/fernet.py $OPTS