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Dockerfile
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# Dockerfile for running nbtools from a pip install
###################################################################################
## NOTE ##
## This Dockerfile mimics a pip install. The Dockerfile that mimics a dev ##
## install has moved to dev.Dockerfile. This prevents an issue where the dev ##
## Dockerfile runs out of memory when transpiling JS dependencies on Binder. ##
###################################################################################
# Pull the latest known good scipy notebook image from the official Jupyter stacks
# Built 02-06-2021
FROM jupyter/scipy-notebook:2021-08-16
MAINTAINER Thorin Tabor <[email protected]>
EXPOSE 8888
#############################################
## ROOT ##
## Install npm ##
#############################################
USER root
RUN apt-get update && apt-get install -y npm
#############################################
## $NB_USER ##
## Install python libraries ##
#############################################
USER $NB_USER
RUN conda install -c conda-forge jupyterlab=3.1.6 voila beautifulsoup4 blas bokeh cloudpickle dask dill h5py hdf5 \
jedi jinja2 libblas libcurl matplotlib nodejs numba numexpr numpy pandas patsy pickleshare pillow pycurl \
requests scikit-image scikit-learn scipy seaborn sqlalchemy sqlite statsmodels sympy traitlets vincent && \
conda install plotly openpyxl sphinx && \
pip install plotnine bioblend jupyterlab-git py4cytoscape
#############################################
## $NB_USER ##
## Build and install nbtools ##
#############################################
RUN pip install ccalnoir cuzcatlan ndex2 hca qgrid ipycytoscape && \
pip install --pre nbtools && \
pip install --pre genepattern-notebook && \
# jupyter nbextension install --py nbtools && \
jupyter nbextension enable --py nbtools --sys-prefix
#############################################
## $NB_USER ##
## Install other labextensions ##
#############################################
RUN jupyter labextension install plotlywidget --no-build && \
jupyter labextension install jupyterlab-plotly --no-build && \
# jupyter labextension install jupyterlab-chart-editor --no-build && \ # JupyterLab 3 not yet supported
jupyter labextension install @aquirdturtle/collapsible_headings && \
# jupyter labextension install jupyter-scribe --no-build && \ # JupyterLab 3 not yet supported
# jupyter labextension install jupyterlab-tabular-data-editor --no-build && \ # JupyterLab 3 not yet supported
printf '\nc.VoilaConfiguration.enable_nbextensions = True' >> /etc/jupyter/jupyter_notebook_config.py
#############################################
## $NB_USER ##
## Launch lab by default ##
#############################################
ENV JUPYTER_ENABLE_LAB="true"
ENV TERM xterm