singularity.def

bootstrap: docker
From: predector/predector-base:1.2.7

%labels
    Author "darcy.ab.jones@gmail.com"
    Version "1.2.7"

%help
    A containter will all dependencies for the predector pipeline.

%setup
    set +x

    ANY_WAS_UNSET=false
    [ -z "${SIGNALP3:-}" ] && ANY_WAS_UNSET=true
    [ -z "${SIGNALP4:-}" ] && ANY_WAS_UNSET=true
    [ -z "${SIGNALP5:-}" ] && ANY_WAS_UNSET=true
    #[ -z "${SIGNALP6:-}" ] && ANY_WAS_UNSET=true
    [ -z "${TARGETP2:-}" ] && ANY_WAS_UNSET=true
    [ -z "${DEEPLOC:-}" ] && ANY_WAS_UNSET=true
    [ -z "${PHOBIUS:-}" ] && ANY_WAS_UNSET=true
    [ -z "${TMHMM:-}" ] && ANY_WAS_UNSET=true

    if [ "${ANY_WAS_UNSET}" = "true" ]
    then
        echo "One or more of the required variables was not set." 1>&2
        echo "Please provide the variables:" 1>&2
        echo -e "- SIGNALP3\n- SIGNALP4\n- SIGNALP5\n- SIGNALP6\n- TARGETP2\n- DEEPLOC\n- PHOBIUS\n- TMHMM" 1>&2
        exit 1
    fi
    mkdir -p "${SINGULARITY_ROOTFS}/onbuild"

    cp "${SIGNALP3}" "${SINGULARITY_ROOTFS}/onbuild/"
    cp "${SIGNALP4}" "${SINGULARITY_ROOTFS}/onbuild/"
    cp "${SIGNALP5}" "${SINGULARITY_ROOTFS}/onbuild/"
    cp "${TARGETP2}" "${SINGULARITY_ROOTFS}/onbuild/"
    cp "${DEEPLOC}" "${SINGULARITY_ROOTFS}/onbuild/"
    cp "${PHOBIUS}" "${SINGULARITY_ROOTFS}/onbuild/"
    cp "${TMHMM}" "${SINGULARITY_ROOTFS}/onbuild/"

    if [ ! -z "${SIGNALP6:-}" ]
    then
        cp "${SIGNALP6}" "${SINGULARITY_ROOTFS}/onbuild/"
    fi

    echo export SIGNALP3="${SIGNALP3:-}" > "${SINGULARITY_ROOTFS}/onbuild/prenv.sh"
    echo export SIGNALP4="${SIGNALP4:-}" >> "${SINGULARITY_ROOTFS}/onbuild/prenv.sh"
    echo export SIGNALP5="${SIGNALP5:-}" >> "${SINGULARITY_ROOTFS}/onbuild/prenv.sh"
    echo export SIGNALP6="${SIGNALP6:-}" >> "${SINGULARITY_ROOTFS}/onbuild/prenv.sh"
    echo export TARGETP2="${TARGETP2:-}" >> "${SINGULARITY_ROOTFS}/onbuild/prenv.sh"
    echo export DEEPLOC="${DEEPLOC:-}" >> "${SINGULARITY_ROOTFS}/onbuild/prenv.sh"
    echo export PHOBIUS="${PHOBIUS:-}" >> "${SINGULARITY_ROOTFS}/onbuild/prenv.sh"
    echo export TMHMM="${TMHMM:-}" >> "${SINGULARITY_ROOTFS}/onbuild/prenv.sh"


%post
    set +x

    ls /
    ls /onbuild

    . /onbuild/prenv.sh
    . /.singularity.d/env/10-docker2singularity.sh
    echo
    signalp3-register "/onbuild/$(basename "${SIGNALP3}")"
    echo
    signalp4-register "/onbuild/$(basename "${SIGNALP4}")"
    echo
    signalp5-register "/onbuild/$(basename "${SIGNALP5}")"
    echo

    if [ ! -z ${SIGNALP6:-} ]
    then
        signalp6-register "/onbuild/$(basename "${SIGNALP6}")"
        echo
    fi

    targetp2-register "/onbuild/$(basename "${TARGETP2}")"
    echo
    deeploc-register "/onbuild/$(basename "${DEEPLOC}")"
    echo
    phobius-register "/onbuild/$(basename "${PHOBIUS}")"
    echo
    tmhmm2-register "/onbuild/$(basename "${TMHMM}")"
    echo

    rm -rf -- /onbuild