Singularity.6.0.5

Bootstrap: docker
From: debian:9-slim

%labels
    AUTHOR krause@mpib-berlin.mpg.de

%post
    mkdir -p /usr/share/man/man1 # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=863199
    echo 'deb http://deb.debian.org/debian stretch main contrib non-free'            > /etc/apt/sources.list
    echo 'deb http://deb.debian.org/debian stretch-updates main contrib non-free'   >> /etc/apt/sources.list
    echo 'deb http://security.debian.org stretch/updates main contrib non-free'     >> /etc/apt/sources.list
    echo 'deb http://deb.debian.org/debian stretch-backports main contrib non-free' >> /etc/apt/sources.list
    apt-get update -y
    DEBIAN_FRONTEND=noninteractive apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" install \
            wget python-minimal libgomp1 ca-certificates \
            libglu1-mesa libgl1-mesa-glx libsm6 libice6 libxt6 \
            libjpeg62-turbo libpng16-16 libxrender1 libxcursor1 \
            libxinerama1 libfreetype6 libxft2 libxrandr2 libmng1 \
            libgtk2.0-0 libpulse0 libasound2 libcaca0 libopenblas-base \
            bzip2 dc bc
    # Cuda 9.1 from stretch-backports
    DEBIAN_FRONTEND=noninteractive apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" install \
            nvidia-cuda-toolkit libcupti-dev nvidia-smi -t stretch-backports
    wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py
    python2 fslinstaller.py -d /usr/local/fsl -V 6.0.5
    echo '/usr/local/fsl/lib' > /etc/ld.so.conf.d/fsl.conf
    ldconfig
    cd /usr/local/fsl/bin && ln -sf eddy_cuda9.1 eddy_cuda
    apt-get clean && apt-get -y autoremove
    rm -f fslinstaller.py
    ln -sf /usr/local/fsl/bin/eddy_cuda9.1 /usr/local/fsl/bin/eddy_cuda

%environment
    FSLDIR=/usr/local/fsl
    . ${FSLDIR}/etc/fslconf/fsl.sh
    PATH=${FSLDIR}/bin:${PATH}
    export FSLDIR PATH