Bootstrap: docker
From: debian:bookworm-slim

%labels
    Author ATGC
    Tool T-Coffee

%help
    Build an Apptainer image for T-Coffee using the Debian package.

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

%post
    set -eu
    export DEBIAN_FRONTEND=noninteractive

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

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

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