Bootstrap: docker
From: debian:trixie-slim

%files
    bmge/runtime.py /opt/myst-plugin/runtime.py
    bmge/engine.py /opt/myst-plugin/engine.py
    bmge/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 default-jdk-headless git
    git clone https://gitlab.pasteur.fr/GIPhy/BMGE.git /tmp/bmge
    git -C /tmp/bmge checkout --detach 4539aa632ce28dedd5828a76abff8cc2d171b976
    mkdir -p /opt/bmge
    cd /tmp/bmge/src
    javac --release 11 BMGE.java
    jar --create --file /opt/bmge/BMGE.jar --main-class BMGE BMGE.class bmge/*.class
    cp /tmp/bmge/COPYING /opt/bmge/
    cp -r /tmp/bmge/src /opt/bmge/
    cd /
    rm -rf /tmp/bmge
    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 bmge