chimp_conda_singularity.def

Bootstrap: docker

From: mambaorg/micromamba

%files
    /home/simonpf/src/chimp/chimp.yml /chimp.yml
    /home/simonpf/src/chimp/aux/singularity_shell_init.sh /singularity_shell_init.sh

%environment
    export PATH="/opt/conda/bin:$PATH"
    export PATH="/opt/conda/envs/chimp/bin:$PATH"

%post

    apt update
    apt install -y git
    micromamba env create -f /chimp.yml
    rm -rf n /chimp.yml
    echo ". /singularity_shell_init.sh" >> $SINGULARITY_ENVIRONMENT
    echo "micromamba activate chimp" >> $SINGULARITY_ENVIRONMENT

%runscript

    exec "$@"