Dockerfile

FROM cookpa/antspynet:latest AS builder

# Use a builder layer to get data and networks. These change infrequently, so can be downloaded
# once and then cached.
USER root

# Copy only files needed to get data and networks
COPY selected_antspynet_data.txt selected_antspynet_networks.txt /opt/

# Get antspynet data that we need
RUN /opt/bin/get_antsxnet_data.py /home/antspyuser/.keras 1 \
        /opt/selected_antspynet_data.txt /opt/selected_antspynet_networks.txt \
    && chmod -R 0755 /home/antspyuser/.keras

FROM cookpa/antspynet:latest AS runtime

ARG DOCKER_IMAGE_TAG="unknown"
ARG DOCKER_IMAGE_VERSION="unknown"

ARG GIT_REMOTE="unknown"
ARG GIT_COMMIT="unknown"

USER root

RUN apt update && apt install -y bc

# Get c3d
COPY --from=pyushkevich/tk:2023b /tk/c3d/build/c3d /opt/bin/c3d
# Get ants
COPY --from=antsx/ants:2.5.4 /opt/ants /opt/ants

COPY scripts/trim_neck.sh /opt/bin/trim_neck.sh
# Copy data and code from builder
COPY --from=builder /home/antspyuser/.keras /home/antspyuser/.keras
COPY . /opt/src/antsnetct

# Install antsnetct
RUN pip install /opt/src/antsnetct \
    && rm -rf /root/.cache/pip

LABEL maintainer="Philip A Cook (https://github.com/cookpa)"
LABEL description="Containerized BIDS cortical thickness pipelines using antspynet."
LABEL git.remote=$GIT_REMOTE
LABEL git.commit=$GIT_COMMIT

ENV GIT_REMOTE=$GIT_REMOTE
ENV GIT_COMMIT=$GIT_COMMIT
ENV DOCKER_IMAGE_TAG=$DOCKER_IMAGE_TAG
ENV DOCKER_IMAGE_VERSION=$DOCKER_IMAGE_VERSION

ENV LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH"
ENV PATH="/opt/bin:/opt/ants/bin:$PATH"

USER antspyuser

ENTRYPOINT ["antsnetct"]
CMD ["-h"]