Dockerfile.server

FROM jupyter/datascience-notebook:hub-3.1.1

# Switch to root user to install tools to build islets and to run bioformats JVM
USER root

RUN apt update --yes && \
    apt upgrade --yes

# Install binaries to install and execute the islets module
RUN apt-get update --yes && \
    apt-get install --yes --no-install-recommends \
    build-essential \
    git \
    bat \
    default-jdk && \
    apt clean

# Switch back to the default user as we do not need root rights anymore and don't want to give them to the user.
USER ${NB_UID}

# Make bat accessible to the user
RUN mkdir -p ~/.local/bin
RUN ln -s /usr/bin/batcat ~/.local/bin/bat

# Upgrade pip and install ffmpeg and tiff dependencies
RUN pip install --upgrade --no-cache pip && \
    pip install --upgrade --no-cache ffmpeg tifffile black isort

# Install graph-tool
RUN conda install -c conda-forge graph-tool

# Install JupyterDash, the corresponding proxy to stream webapps, and needed labextension
RUN pip install --upgrade --no-cache \
        dash jupyter-dash jupyter-server-proxy \
        jupyterlab-drawio jupyter-archive jupyter-resource-usage jupyterlab-spreadsheet-editor \
        jupyterlab-code-formatter jupyterlab-system-monitor jupyterlab_templates
RUN jupyter labextension install jupyterlab-plotly
RUN jupyter lab build
RUN echo "c.JupyterLabTemplates.template_dirs = ['/data/useful/templates']" >> ${HOME}/.jupyter/jupyter_notebook_config.py
RUN echo "c.JupyterLabTemplates.include_default = False" >> ${HOME}/.jupyter/jupyter_notebook_config.py

# Switch to root user to install tools to build islets and to run bioformats JVM
USER root

# Install the islets module
COPY . /opt/islets/Physio_Ca/
WORKDIR /opt/islets/Physio_Ca/
RUN pip install .
RUN chmod +x /opt/islets/Physio_Ca/scripts/full_process.py

# Create a directory to copy the islets source into it.
# The directory will have fixed permissions.
RUN /usr/local/bin/fix-permissions /opt/islets/
RUN chown -R ${NB_UID}:users ${HOME}

# Switch back to the default user as we do not need root rights anymore and don't want to give them to the user.
USER ${NB_UID}

# Link to data and set the home directory as default work directory
WORKDIR ${HOME}/work
RUN ln -s /data ${HOME}/work/local_data