Dockerfile

FROM python:3.8-buster

# Base packages

RUN apt-get update&& \
    apt-get -y install graphviz build-essential python-dev ffmpeg fish
    
RUN pip install --upgrade pip

# Install jupyter notebook
RUN pip3 install jupyter jupyterlab

# Install viz dependencies
RUN pip3 install matplotlib ipyvolume seaborn

# Lock to datajoint 0.12.9
RUN pip3 install datajoint==0.12.9

# Install the outside packages
WORKDIR /src
COPY README.md /microns-nda-access/.
COPY Dockerfile /microns-nda-access/.
COPY docker-compose.yml /microns-nda-access/.
RUN git clone --depth 1 --branch v8 https://github.com/cajal/microns_phase3_nda
RUN pip3 install torch==1.9.0+cpu torchvision==0.10.0+cpu torchaudio==0.9.0 -f https://download.pytorch.org/whl/torch_stable.html
RUN pip3 install -e microns_phase3_nda/
RUN pip3 install git+https://github.com/AllenInstitute/em_coregistration.git@phase3

# Set up work environment
WORKDIR /notebooks
COPY README.md .
RUN mkdir tutorial_notebooks/ && cp -r /src/microns_phase3_nda/tutorial_notebooks/. tutorial_notebooks/.
RUN mkdir workspace/

# Start jupyter notebook
RUN mkdir -p /scripts \
    && mkdir -p /root/.jupyter/custom/

# The configuration files are placed here to avoid more file dependencies. Quite messy, but should work the same.

RUN echo "#!/usr/bin/env bash \n\
\n\
jupyter lab "$@" --allow-root\n" \
>> /scripts/run_jupyter.sh

RUN echo "# Accept all incoming requests \n\
c.NotebookApp.ip = '0.0.0.0' \n\
c.NotebookApp.port = 8888 \n\
c.NotebookApp.open_browser = False \n\
c.MultiKernelManager.default_kernel_name = 'python3' \n\
c.NotebookApp.token = '' \n\
c.NotebookApp.password = ''\n" \
>> /root/.jupyter/jupyter_notebook_config.py

RUN echo ".container { \n\
    width: 75% !important; \n\
} \n\
\n\
div.cell.selected { \n\
    border-left-width: 1px !important; \n\
} \n\
\n\
div.output_scroll { \n\
    resize: vertical !important; \n\
}\n" \
>> /root/.jupyter/custom/custom.css

RUN chmod -R a+x /scripts
ENTRYPOINT ["/scripts/run_jupyter.sh"]