Dockerfile

# syntax=docker/dockerfile:1.4

FROM nipreps/fmriprep:20.2.7

RUN mkdir /ext /host \
 && chmod a+rwx /ext /host

ENV PATH="/usr/local/miniconda/bin:$PATH" \
    MAMBA_EXE="/usr/local/miniconda/bin/mamba"

# Use `/var/cache` for downloaded resources instead of
# `/home/fmriprep/.cache`, because it is less likely to be
# obscured by default container bind mounts when running
# with Singularity
ENV XDG_CACHE_HOME="/var/cache" \
    HALFPIPE_RESOURCE_DIR="/var/cache/halfpipe" \
    TEMPLATEFLOW_HOME="/var/cache/templateflow"
RUN mv /home/fmriprep/.cache/templateflow /var/cache

# Re-install `conda` and all `python` packages
RUN --mount=source=requirements.txt,target=/requirements.txt \
    --mount=source=install-requirements.sh,target=/install-requirements.sh \
    rm -rf /usr/local/miniconda \
 && curl --show-error --location \
        "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh" \
        --output /tmp/miniconda.sh \
 && bash /tmp/miniconda.sh -b -p /usr/local/miniconda \
 && mamba install --yes "python=3.11" "pip" "gdb" "nodejs" "gsl" \
 && /install-requirements.sh \
        --requirements-file /requirements.txt \
 && sync \
 && mamba clean --yes --all --force-pkgs-dirs \
 && sync \
 && find /usr/local/miniconda/ -follow -type f -name "*.a" -delete \
 && rm -rf ~/.conda \
        /var/cache/apt /var/lib/apt \
        ~/.cache/pip /var/cache/pip \
        /tmp/* /var/tmp/* \
 && sync

# Re-apply matplotlib settings after updating
# Taken from `fmriprep`
# Pre-caches fonts, set 'Agg' as default backend for matplotlib
RUN python -c "from matplotlib import font_manager" \
 && sed -i '/backend:/s/^#*//;/^backend/s/: .*/: Agg/' \
        $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )

# Download all resources
RUN --mount=source=src/halfpipe/resource.py,target=/resource.py \
    python /resource.py

# Add coinstac server components
COPY --from=coinstacteam/coinstac-base:latest /server/ /server/

# Install HALFpipe
RUN --mount=target=/src/halfpipe \
    cp -r /src/halfpipe /tmp \
 && pip install --no-deps /tmp/halfpipe \
 && rm -rf ~/.cache/pip /var/cache/pip /tmp/* /var/tmp/* \
 && sync

ENTRYPOINT ["/usr/local/miniconda/bin/halfpipe"]