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Dockerfile-ci
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Dockerfile-ci
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# syntax=docker/dockerfile:1
FROM python:3.12-slim
LABEL org.opencontainers.image.source=https://github.com/juaml/junifer
LABEL org.opencontainers.image.description="Junifer CI container image"
LABEL org.opencontainers.image.licenses=AGPL-3.0-only
RUN apt-get update && \
apt-get install -y \
pkg-config \
gcc \
git \
make \
curl \
# ANTs runtime stuff
libhdf5-dev \
bc \
# AFNI runtime stuff
libf2c2-dev \
libglew-dev \
libglib2.0-dev \
libglu1-mesa-dev \
libglw1-mesa-dev \
libgsl-dev \
libgts-dev \
libjpeg62-turbo-dev \
libmotif-dev \
libxi-dev \
libxmhtml-dev \
libxmu-dev \
libxpm-dev \
libxt-dev \
netpbm \
libjpeg-progs \
qhull-bin \
r-base \
tcsh \
xvfb \
# FSL runtime stuff
file \
dc \
libquadmath0 \
libgomp1
# Add xfms
COPY --from=ghcr.io/juaml/human-template-xfms:main /opt/xfms /root/junifer/data/xfms
# Add ANTs
COPY --from=antsx/ants:latest /opt/ants /opt/ants
# Set env vars for ANTs
ENV PATH="/opt/ants/bin:$PATH" \
LD_LIBRARY_PATH="/opt/ants/lib"
# Add AFNI
COPY --from=afni/afni_make_build:latest /opt/afni/install /opt/afni/bin
# Set env vars for AFNI
ENV PATH="/opt/afni/bin:$PATH"
# Patch gsl
RUN ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.23
# Add FSL
RUN curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | \
python - -d /opt/fsl/ --skip_registration
# Set env vars for FSL
ENV FSLDIR=/opt/fsl \
FSLOUTPUTTYPE=NIFTI_GZ \
PATH="/opt/fsl/share/fsl/bin:$PATH"
# Clean apt cache
RUN apt-get autoremove --purge && apt-get clean