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/    
    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 "$@"