FROM python:3.12-slim-bookworm

LABEL org.opencontainers.image.source=https://github.com/juaml/junifer

LABEL org.opencontainers.image.description="Junifer container image"

LABEL org.opencontainers.image.licenses=AGPL-3.0-only

RUN apt-get update && \

apt-get install -y \

pkg-config \

gcc \

git \

git-annex \

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 \

&& rm -rf /var/lib/apt/lists/*

COPY --from=ghcr.io/juaml/junifer-data:v7 /opt/junifer-data /root/junifer_data/v7

COPY --from=antsx/ants:latest /opt/ants /opt/ants

ENV PATH="/opt/ants/bin:$PATH" \

LD_LIBRARY_PATH="/opt/ants/lib"

COPY --from=afni/afni_make_build:latest /opt/afni/install /opt/afni/bin

ENV PATH="/opt/afni/bin:$PATH"

RUN ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.23

RUN curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | \

python - -d /opt/fsl/ --skip_registration

ENV FSLDIR=/opt/fsl \

FSLOUTPUTTYPE=NIFTI_GZ \

PATH="/opt/fsl/share/fsl/bin:$PATH"

RUN apt-get autoremove --purge && apt-get clean

RUN python -m pip install --no-cache-dir --upgrade pip setuptools wheel

RUN git clone --depth 1 --recurse-submodules https://github.com/juaml/junifer.git && \

cd junifer && \

python -m pip install --no-cache-dir ".[all]" && \

cd .. && rm -rf junifer