Singularity

Bootstrap: docker
From: debian:buster-slim

%environment
    export LC_ALL=C.UTF-8
    export BGDATA_OFFLINE=TRUE

%runscript
    exec "/boostdm/run.sh" "$@"

%setup
    mkdir ${SINGULARITY_ROOTFS}/boostdm
    cp boostwrap-develop.zip ${SINGULARITY_ROOTFS}/boostdm/
    cp runner.sh ${SINGULARITY_ROOTFS}/usr/bin
    chmod a+rx ${SINGULARITY_ROOTFS}/usr/bin/runner.sh

%post
    apt-get update
    apt-get -y install locales-all zlib1g-dev python3 python3-dev \
    python3-pip python3-dill python3-numpy python3-pandas \
    python3-sklearn python3-pycurl python3-pybedtools python3-pybigwig \
    python3-matplotlib python3-click python3-tqdm python3-pygraphviz \
    python3-networkx tabix bedtools

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

    /usr/bin/pip3 install xgboost==0.90 shap==0.35 ipython pillow bgreference pytabix==0.0.2 bgvep pyliftover scikit-optimize seaborn bgoncotree
    /usr/bin/pip3 install /boostdm/boostwrap-develop.zip