Bootstrap: docker
From: continuumio/miniconda3

%labels
    Author ATGC
    Tool TFScope

%post
    set -e
    export DEBIAN_FRONTEND=noninteractive

    apt-get update
    apt-get install -y --no-install-recommends \
        git \
        ca-certificates \
        wget
    apt-get clean
    rm -rf /var/lib/apt/lists/*

    # Fetch upstream TFScope sources (override with TFSCOPE_REPO/TFSCOPE_REF if needed)
    TFSCOPE_REPO="${TFSCOPE_REPO:-https://gite.lirmm.fr/rromero/tfscope.git}"
    TFSCOPE_REF="${TFSCOPE_REF:-main}"
    git clone --depth 1 --branch "${TFSCOPE_REF}" "${TFSCOPE_REPO}" /opt/tfscope

    # Create the conda environment as defined by the upstream Dockerfile/environment.yml
    conda config --set channel_priority strict
    conda config --remove-key channels || true
    conda config --add channels conda-forge
    conda config --add channels bioconda
    conda config --add channels defaults
    conda install -n base -c conda-forge -y mamba
    cd /opt/tfscope
    MAMBA_NO_BANNER=1 mamba env create --override-channels -c conda-forge -c bioconda -c defaults -f code/environment.yml
    conda clean -afy

%environment
    export PATH=/opt/conda/envs/tfscope/bin:$PATH
    export MPLCONFIGDIR=/tmp/matplotlib

%runscript
    exec conda run --no-capture-output -n tfscope python /opt/tfscope/code/TFscope_main.py "$@"