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Dockerfile
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FROM jupyter/scipy-notebook:68d2d835fb16
USER root
RUN mkdir /opt/config
RUN mkdir /home/jovyan/base
ADD requirements.txt /opt/config
RUN pip install spacy
RUN python -m spacy download en_core_web_trf
# Install a few dependencies for iCommands, text editing, and monitoring instances
RUN apt-get update && apt-get install -y \
apt-transport-https \
gcc \
gnupg \
htop \
less \
libfuse2 \
libpq-dev \
libssl1.0 \
lsb \
nano \
nodejs \
software-properties-common \
vim
RUN python -m pip install requests
# Install iCommands
# RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - \
# && echo "deb [arch=amd64] https://packages.irods.org/apt/ bionic main" | tee /etc/apt/sources.list.d/renci-irods.list \
# && apt-get update && apt-get install -y irods-runtime irods-icommands
# Install Jupyter SQL
RUN pip install ipython-sql jupyterlab_sql psycopg2 \
&& conda update -n base conda \
&& conda install -c conda-forge nodejs \
&& jupyter serverextension enable jupyterlab_sql --py --sys-prefix \
&& jupyter lab build
# install the irods plugin for jupyter lab -- non-functional beyond JupyterLab v1.0.9
RUN pip install jupyterlab_irods \
&& jupyter serverextension enable --py jupyterlab_irods \
&& jupyter labextension install ijab
# install jupyterlab hub-extension, lab-manager, bokeh
RUN jupyter lab --version \
&& jupyter labextension install --debug @jupyter-widgets/jupyterlab-manager
# install jupyterlab git extension
RUN jupyter labextension install @jupyterlab/git && \
pip install --upgrade jupyterlab-git && \
jupyter serverextension enable --py jupyterlab_git
# install jupyterlab github extension
RUN jupyter labextension install @jupyterlab/github
RUN jupyter labextension install @pyviz/jupyterlab_pyviz
# Install and configure jupyter lab.
COPY jupyter_notebook_config.json /opt/conda/etc/jupyter/jupyter_notebook_config.json
# Add the jovyan user to UID 1000
RUN groupadd jovyan && usermod -aG jovyan jovyan && usermod -d /home/jovyan -u 1000 jovyan
RUN chown -R jovyan:jovyan /home/jovyan
# copy over program files
RUN pip install jupyterlab
RUN pip install -r /opt/config/requirements.txt
RUN pip install ipywidgets
WORKDIR /home/jovyan/base
COPY find_similarities/ find_similarities/
COPY vectorize_docs/ vectorize_docs/
COPY annotate/ annotate/
COPY train_model/ train_model/
RUN chmod -R 777 /home/jovyan/base
RUN jupyter serverextension enable --py jupyterlab --sys-prefix
USER jovyan
RUN mkdir /home/jovyan/test_dir
EXPOSE 8888
COPY entry.sh /bin
RUN mkdir -p /home/jovyan/.irods
ENTRYPOINT ["bash", "/bin/entry.sh"]