mofid.def

Bootstrap: docker
From: continuumio/miniconda3

%files
    . /mofid  # WARNING: relative path based on where singularity build is called

%post
    # set up conda and deps, per .travis.yml
    apt-get update -qq
    mkdir -p /usr/share/man/man1/  # required to prevent default-jre installation from crashing
    apt-get install -qq default-jre
    apt-get install -qq build-essential cmake

    conda config --set always_yes yes --set changeps1 no
    conda create -q -n py2 python=2.7

    # copy source code from git
    cd /mofid

    # compile openbabel, C++ analysis code, and Python package
    make init
    python set_paths.py
    pip install .

%runscript
    if [ $# -lt 2 ]
    then
        echo "USAGE: need to specify a command (file or folder), followed by path(s)" 1>&2 && exit
    fi
    COMMAND="$1"
    if [ "$COMMAND" = "file" ]
    then
        python /mofid/Python/run_mofid.py "$2" "Output" json  # writing json to stdout
    elif [ "$COMMAND" = "folder" ]
    then
        MOFID_INPUT_DIR=$(realpath "$2")  # relative path -> abspath
        if [ $# -lt 3 ]
        then
            MOFID_OUTPUT_DIR="$PWD/Output"
        else
            MOFID_OUTPUT_DIR=$(realpath "$3")
        fi
        cd /mofid  # because run_folder.sh has some hard-coded relative paths
        Scripts/run_folder.sh "$MOFID_INPUT_DIR" "$MOFID_OUTPUT_DIR"
    else
        echo "Unknown command. Select 'file' for a single json output or 'folder' for bulk analysis" 1>&2 && exit
    fi

%test
    # Writes to Output/ within a temporary directory
    TMP_TEST_DIR=$(mktemp -d -t mofid-test-XXXXXXXXXX)
    echo "Writing test output to $TMP_TEST_DIR/Output"
    cd "$TMP_TEST_DIR"
    python /mofid/tests/check_run_mofid.py
    python /mofid/tests/check_mof_composition.py
    cd
    rm -r "$TMP_TEST_DIR"