Bootstrap: docker
From: debian:bookworm-slim

%labels
    Author ATGC
    Tool TNT

%help
    Build a TNT Apptainer image by downloading the upstream TNT Linux archive
    during the image build.

    Upstream archive:
      https://www.lillo.org.ar/phylogeny/tnt/tnt-linux.zip

    Note:
      TNT licensing may restrict redistribution of the resulting image.

%files
    tnt/container_entrypoint.bash /usr/local/bin/tnt-entrypoint

%post
    set -eu
    export DEBIAN_FRONTEND=noninteractive

    apt-get update
    apt-get install -y --no-install-recommends \
        bash \
        ca-certificates \
        python3 \
        unzip \
        wget
    apt-get clean
    rm -rf /var/lib/apt/lists/*

    chmod 0755 /usr/local/bin/tnt-entrypoint

    mkdir -p /tmp/tnt-build /opt/tnt-src /opt/tnt

    archive="/tmp/tnt-build/tnt-linux.zip"
    wget -O "${archive}" "https://www.lillo.org.ar/phylogeny/tnt/tnt-linux.zip"

    unzip -q "${archive}" -d /opt/tnt-src

    tnt_binary="$(find /opt/tnt-src -type f -path '*/TNT-bin/tnt' | head -n1)"
    if [ -z "${tnt_binary}" ]; then
        echo "Unable to locate TNT-bin/tnt in the downloaded archive." >&2
        exit 1
    fi

    install_root="$(dirname "$(dirname "${tnt_binary}")")"
    cp -a "${install_root}/." /opt/tnt/

    chmod -R a+rX /opt/tnt
    chmod 0755 /opt/tnt/TNT-bin/tnt

    rm -rf /opt/tnt-src /tmp/tnt-build

%environment
    export TNT_HOME=/opt/tnt
    export PATH=/opt/tnt/TNT-bin:$PATH
    export LD_LIBRARY_PATH=/opt/tnt/TNT-bin${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}

%runscript
    exec /usr/local/bin/tnt-entrypoint "$@"