Dockerfile

# Jupyter container used for Galaxy IPython (+other kernels) Integration
FROM pangeo/pangeo-notebook:2023.02.27

MAINTAINER Anne Fouilloux, annef@simula.no

ENV DEBIAN_FRONTEND noninteractive

# Install system libraries first as root
USER root

RUN apt-get -qq update && apt-get install --no-install-recommends -y libcurl4-openssl-dev libxml2-dev \
    apt-transport-https python-dev-is-python3 libc-dev pandoc pkg-config liblzma-dev libbz2-dev libpcre3-dev \
    build-essential libblas-dev liblapack-dev gfortran libzmq3-dev libyaml-dev libxrender1 fonts-dejavu \
    libfreetype6-dev libpng-dev net-tools procps libreadline-dev wget software-properties-common octave \
    ca-certificates wget vim subversion sshfs openssh-client \
    # IHaskell dependencies
    zlib1g-dev libtinfo-dev libcairo2-dev libpango1.0-dev && \
    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

USER $NB_USER

# Python packages
RUN conda update -n base conda && conda clean -yt && \
    pip install --no-cache-dir bioblend galaxy-ie-helpers 

ADD ./startup.sh /startup.sh
ADD ./get_notebook.py /get_notebook.py

# We can get away with just creating this single file and Jupyter will create the rest of the
# profile for us.
RUN mkdir -p /home/$NB_USER/.ipython/profile_default/startup/

COPY ./ipython-profile.py /home/$NB_USER/.ipython/profile_default/startup/00-load.py
COPY jupyter_notebook_config.py /home/$NB_USER/.jupyter/
COPY jupyter_lab_config.py /home/$NB_USER/.jupyter/

ADD ./default_notebook.ipynb /home/$NB_USER/notebook.ipynb

# ENV variables to replace conf file
ENV DEBUG=false \
    GALAXY_WEB_PORT=10000 \
    NOTEBOOK_PASSWORD=none \
    CORS_ORIGIN=none \
    DOCKER_PORT=none \
    API_KEY=none \
    HISTORY_ID=none \
    REMOTE_HOST=none \
    GALAXY_URL=none


# Install the Dask dashboard
RUN pip install dask-labextension

# Dask Scheduler & Bokeh ports
EXPOSE 8787
EXPOSE 8786

USER root

RUN apt-get -qq update && \
    apt-get install -y net-tools procps && \
    apt-get autoremove -y && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# /import will be the universal mount-point for Jupyter
# The Galaxy instance can copy in data that needs to be present to the Jupyter webserver
RUN mkdir -p /import/jupyter/outputs/ && \
    mkdir -p /import/jupyter/data && \
    mkdir /export/ && \
    chown -R $NB_USER:users /home/$NB_USER/ /import /export/

ENV USER=$NB_USER

WORKDIR /import

# Start Jupyter Notebook
CMD /startup.sh