singularity.build

Bootstrap: docker
From: ubuntu:17.10 

%help
    Singularity image based on ubuntu 17.10 with libraries for running CCB-ID
    Maintained by Christopher Anderson (cbanders@stanford.edu) @christobal54

%labels
    Maintainer Christopher Anderson
    Website https://github.com/stanford-ccb/ccb-id
    Version 0.1.0

%setup
    # set the default directory for storing configuration files
    mkdir $SINGULARITY_ROOTFS/ccb
    
%files
    requirements.txt

%environment
    # make sure you have a $CCBID environment variable set on your local machine
    #  that points to the ccb-id base directory
    
    # here we set the path, python path, and ipython path to access the ccb-id install
    export PYTHONPATH=$CCBID:$PYTHONPATH
    export PATH=$CCBID/bin:$PATH
    export IPYTHONDIR=$CCBID/ipython

%post
    # set the default directory for storing configuration files
    #export CCB=/ccb
    #cd $CCB

    # install packages via apt
    apt-get update -y
    apt-get install -y \
        python-gdal \
        gdal-bin \
        libgdal20 \
        ipython \
        python-setuptools \
        python-dev \
        python-pip \
        python-tk \
        build-essential \
        libfontconfig1 \
        mesa-common-dev \
        python-numpy \
        python-scipy \
        python-pandas \
        python-geopandas \
        python-qt4 \
        python-sip \
        python-pyside \
        python-h5py \
        gcc \
        gfortran \
        qt5.1 \
        git \
        vim

    # clean up the apt files
    apt-get clean 
    rm -rf /var/lib/apt/lists/*

    # install pip packages
    pip install matplotlib \
        qtpy \
        Pyro4 \
        psutil \
        rtree \
        qtawesome \
        qtpy \
        six \
        taskgraph \
        Pyro4 

    # install ccb-id from git repo
    #git clone https://github.com/stanford-ccb/ccb-id.git
    
    # install the ccb-id dependencies
    #pip install -r ccb-id/requirements.txt
    pip install -r requirements.txt
    
    # that's all, folks!

%runscript
    echo "--- CCB-ID ---"
    exec "$@"