Bootstrap: docker
From: debian:trixie-slim

%files
    fastme/distance_runtime.py /opt/myst-plugin/distance_runtime.py
    fastme/distance_engine.py /opt/myst-plugin/distance_engine.py
    fastme/distance_input.py /opt/myst-plugin/distance_input.py
    fastme/distance_options.json /opt/myst-plugin/distance_options.json
    fastme/tree_output.py /opt/myst-plugin/tree_output.py

%post
    set -eu
    export DEBIAN_FRONTEND=noninteractive
    apt-get update
    apt-get install -y --no-install-recommends phylip=1:3.697+dfsg-4 python3 python3-biopython python3-venv ca-certificates
    python3 -m venv --system-site-packages /opt/distance-env
    /opt/distance-env/bin/pip install commonnexus==2.0.0
    dpkg-query -W > /opt/myst-plugin/packages.tsv
    /opt/distance-env/bin/pip freeze > /opt/myst-plugin/python-packages.txt
    apt-get install -y --no-install-recommends build-essential git autoconf automake libtool
    git clone https://gite.lirmm.fr/atgc/FastME.git /opt/FastME
    cd /opt/FastME
    git checkout --detach 08e2150495640a45b89fb816edd894bec8219186
    autoreconf -fi
    ./configure
    make -j2
    cp src/fastme /usr/local/bin/
    git rev-parse HEAD > /opt/myst-plugin/fastme-source-commit.txt
    rm -rf /var/lib/apt/lists/*

%environment
    export OMP_NUM_THREADS=1
    export OPENBLAS_NUM_THREADS=1

%runscript
    if [ "${1:-}" = "--bionj-pipeline" ]; then
        shift
        exec /opt/distance-env/bin/python /opt/myst-plugin/distance_runtime.py "$@"
    fi
    exec fastme "$@"

%test
    test -x /usr/lib/phylip/bin/neighbor
    /opt/distance-env/bin/python -c 'from Bio import AlignIO, Phylo; from commonnexus import Nexus'

%labels
    Author ATGC