Bootstrap: docker
From: debian:trixie-slim

%files
    3dcoffee/runtime.py /opt/myst-plugin/runtime.py
    3dcoffee/engine.py /opt/myst-plugin/engine.py
    3dcoffee/config.json /opt/myst-plugin/config.json

%post
    set -eu
    export DEBIAN_FRONTEND=noninteractive
    apt-get update
    apt-get install -y --no-install-recommends python3 python3-biopython ca-certificates
    apt-get install -y --no-install-recommends t-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 tm-align=20190822+dfsg-3 python3-requests perl libwww-perl clustalw
    dpkg-query -W > /opt/myst-plugin/packages.tsv
    rm -rf /var/lib/apt/lists/*

%environment
    export OMP_NUM_THREADS=1
    export OPENBLAS_NUM_THREADS=1

%runscript
    exec python3 /opt/myst-plugin/runtime.py "$@"

%test
    python3 -c 'from Bio import AlignIO, Phylo, SeqIO'
    test -s /opt/myst-plugin/config.json

%labels
    Author ATGC
    Tool 3dcoffee