babs-input-overlay-helper.def

Bootstrap: docker
From: ubuntu:22.04

%labels
    Author babs
    Description BABS helper image for overlay-mode DataLad operations

%post
    set -e
    export DEBIAN_FRONTEND=noninteractive
    apt-get update
    apt-get install -y --no-install-recommends \
        bash \
        ca-certificates \
        coreutils \
        datalad \
        git \
        git-annex \
        gnupg \
        lsb-release \
        python3 \
        python3-pip \
        sed \
        util-linux

    # Try to provide Apptainer/Singularity in the helper image. We normalize on
    # "singularity" because participant_job.sh calls singularity.
    # 1) Default repos (e.g. Neurodebian, or distro that ships apptainer).
    if apt-cache show apptainer >/dev/null 2>&1; then
        apt-get install -y --no-install-recommends apptainer && \
            ln -sf /usr/bin/apptainer /usr/local/bin/singularity || true
    elif apt-cache show singularity-container >/dev/null 2>&1; then
        apt-get install -y --no-install-recommends singularity-container || true
    fi
    # 2) Fallback: install from official Apptainer PPA when not in default repos.
    if ! command -v singularity >/dev/null 2>&1 && ! command -v apptainer >/dev/null 2>&1; then
        ( set +e
          apt-get install -y --no-install-recommends software-properties-common
          add-apt-repository -y ppa:apptainer/ppa
          apt-get update
          apt-get install -y --no-install-recommends apptainer
          ln -sf /usr/bin/apptainer /usr/local/bin/singularity
        ) || true
    fi

    apt-get clean
    rm -rf /var/lib/apt/lists/*

%environment
    export LC_ALL=C
    export LANG=C

%test
    set -e
    command -v bash
    command -v datalad
    command -v git
    command -v git-annex
    command -v singularity || command -v apptainer