Singularity.v3.2

Bootstrap: docker
From: ubuntu:16.04

%post
    apt-get update
    apt-get install -y  wget bzip2
    mkdir -p /app
    # install anaconda
    if [ ! -d /app/anaconda ]; then
        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
        -O /app/anaconda.sh && \
        bash /app/anaconda.sh -b -p /app/anaconda && \
        rm -rf /app/anaconda.sh
    fi

    apt-get clean && \
    apt-get autoclean && \
    rm -rf /var/lib/apt/lists/*
    # now do not delete /tmp/* /var/tmp/* files, as they are mounted from the HOST system.
    # see: https://github.com/linzhi2013/MitoZ/issues/119

    # set anaconda path
    export PATH="/app/anaconda/bin:$PATH"

    conda config --add channels defaults
    conda config --add channels bioconda
    conda config --add channels conda-forge

    conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!

    # mamba install -c bioconda mitoz
    # or local installation:
    mamba install -f https://github.com/linzhi2013/MitoZ/releases/download/3.2/mitozEnv.yaml
    pip install https://github.com/linzhi2013/MitoZ/releases/download/3.2/mitoz-3.2.tar.gz

    conda clean -y -a



%environment
    export LC_ALL=C
    export PATH=/app/anaconda/bin:$PATH


%runscript
    mitoz "$@"


%labels
AUTHOR    Guanliang MENG, ZFMK