VAMPIRE/vampire.def at main · Zikun-Yang/VAMPIRE · GitHub

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Bootstrap: docker
From: ubuntu:22.04

%labels
    Author Zikun-Yang
    Version v0.4.2

%help
    VAMPIRE - tandem repeat motif annotation tool

    Build options:
      Default (international users):
        apptainer build vampire.sif vampire.def

      Chinese users (use Tsinghua mirrors for conda + pip):
        apptainer build --build-arg CONDA_MIRROR=cn vampire.sif vampire.def

      Install a specific version:
        apptainer build --build-arg VAMPIRE_VERSION=0.4.2 vampire.sif vampire.def

%arguments
    VAMPIRE_VERSION=""
    CONDA_MIRROR=""

%post
    set -e

    # Runtime libraries for Python scientific / plotting wheels and Miniconda
    apt-get update && apt-get install -y \
        ca-certificates \
        wget \
        curl \
        bzip2 \
        libcurl4 \
        libfontconfig1 \
        libfreetype6 \
        libpng16-16 \
        libtiff5 \
        libjpeg-turbo8 \
        locales

    locale-gen en_US.UTF-8
    update-locale LANG=en_US.UTF-8

    # Install Miniconda
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh
    bash /tmp/miniconda.sh -b -p /opt/conda
    rm /tmp/miniconda.sh
    export PATH="/opt/conda/bin:$PATH"

    # Configure conda + pip channels with optional mirror support
    # Set CONDA_MIRROR=cn before building to use Tsinghua (TUNA) mirrors.
    if [ "{{ CONDA_MIRROR }}" = "cn" ]; then
        echo "==> Configuring Tsinghua (TUNA) mirrors for Chinese network"
        TUNA="https://mirrors.tuna.tsinghua.edu.cn/anaconda"
        /opt/conda/bin/conda config --remove-key channels || true
        /opt/conda/bin/conda config --add channels "${TUNA}/cloud/bioconda/"
        /opt/conda/bin/conda config --add channels "${TUNA}/cloud/conda-forge/"
        /opt/conda/bin/conda config --add channels "${TUNA}/pkgs/main/"
        /opt/conda/bin/conda config --set show_channel_urls yes
        /opt/conda/bin/pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
        /opt/conda/bin/pip config set global.trusted-host pypi.tuna.tsinghua.edu.cn
    else
        echo "==> Configuring official conda channels (international)"
        /opt/conda/bin/conda config --add channels conda-forge
        /opt/conda/bin/conda config --add channels bioconda
        /opt/conda/bin/conda config --set show_channel_urls yes
    fi

    /opt/conda/bin/conda init bash
    /opt/conda/bin/conda clean -afy

    # Install bioinformatics dependencies
    /opt/conda/bin/conda install -y mafft

    # Install VAMPIRE (specific version if provided, otherwise latest stable)
    if [ -n "{{ VAMPIRE_VERSION }}" ]; then
        /opt/conda/bin/pip install --root-user-action=ignore "vampire-tr=={{ VAMPIRE_VERSION }}"
    else
        /opt/conda/bin/pip install --root-user-action=ignore vampire-tr
    fi

    # Clean up
    /opt/conda/bin/conda clean -afy
    apt-get clean && rm -rf /var/lib/apt/lists/*

%environment
    export LANG=en_US.UTF-8
    export LC_ALL=en_US.UTF-8
    export PATH=/opt/conda/bin:/usr/local/bin:$PATH
    export PYTHONUNBUFFERED=1

%runscript
    echo "VAMPIRE v0.4.2 - tandem repeat motif annotation"
    exec "$@"