Bootstrap: docker
From: debian:trixie

%labels
    Author ATGC

%post
    set -e
    export DEBIAN_FRONTEND=noninteractive
    apt-get update && apt-get upgrade -y
    apt-get install -y \
        build-essential wget git autoconf automake libtool openmpi-bin libopenmpi-dev \
        bc dos2unix r-base-core ca-certificates unzip make cmake
    cd /opt
    git clone https://gite.lirmm.fr/atgc/sms.git
    cd sms
    cd tarball
    unzip sms-2.1.1.zip
    cd sms-2.1.1/    
    # Modern R rejects order(data.frame); order the numeric distance column.
    grep -Fq 'row.names(d)[order(d)]' chi.R
    sed -i 's/order(d)/order(d[[1]])/' chi.R
    # Sort numeric scores before converting decimal points for the CSV export.
    sed -i -E "s/tr '\\.' ',' \\| sort -g -k ([78])/LC_ALL=C sort -g -k \\1 | tr '.' ','/g" sms.sh
    make
    chmod +x *.sh
    mkdir workspace

%environment
    export PATH=/opt/sms/tarball/sms-2.1.1:$PATH
    export SHELL=/bin/bash

%runscript
    exec /bin/bash /opt/sms/tarball/sms-2.1.1/sms.sh "$@"