updated singleuser configs for other image builds.
This commit is contained in:
M. Pilosov
parent
f7760967a6
commit
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244
singleuser/Dockerfile-Fenics
Executable file
244
singleuser/Dockerfile-Fenics
Executable file
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ARG DOCKER_NOTEBOOK_IMAGE
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FROM $DOCKER_NOTEBOOK_IMAGE
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ARG JUPYTERHUB_VERSION
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# Install vim in case someone wants to use the terminal
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USER root
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RUN apt-get update && \
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apt-get install -y vim && \
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apt-get install -y gcc && \
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rm -rf /var/lib/apt/lists/*
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RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse
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#any additional installations go here.
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LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
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ARG NB_USER="student"
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ARG NB_UID="1001"
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ARG NB_GID="100"
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USER root
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# Install all OS dependencies for notebook server that starts but lacks all
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# features (e.g., download as all possible file formats)
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ENV DEBIAN_FRONTEND noninteractive
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RUN apt-get update && apt-get -yq dist-upgrade \
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&& apt-get install -yq --no-install-recommends \
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wget \
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bzip2 \
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ca-certificates \
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sudo \
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locales \
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fonts-liberation \
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&& rm -rf /var/lib/apt/lists/*
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RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
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locale-gen
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# Configure environment
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ENV CONDA_DIR=/opt/conda \
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SHELL=/bin/bash \
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NB_USER=$NB_USER \
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NB_UID=$NB_UID \
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NB_GID=$NB_GID \
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LC_ALL=en_US.UTF-8 \
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LANG=en_US.UTF-8 \
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LANGUAGE=en_US.UTF-8
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ENV PATH=$CONDA_DIR/bin:$PATH \
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HOME=/home/$NB_USER
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ADD fix-permissions /usr/local/bin/fix-permissions
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# Create jovyan user with UID=1000 and in the 'users' group
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# and make sure these dirs are writable by the `users` group.
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RUN groupadd wheel -g 11 && \
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echo "auth required pam_wheel.so use_uid" >> /etc/pam.d/su && \
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useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
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mkdir -p $CONDA_DIR && \
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chown $NB_USER:$NB_GID $CONDA_DIR && \
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chmod g+w /etc/passwd && \
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fix-permissions $HOME && \
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fix-permissions $CONDA_DIR
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USER $NB_UID
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# Setup work directory for backward-compatibility
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RUN mkdir /home/$NB_USER/work && \
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fix-permissions /home/$NB_USER
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# Install conda as jovyan and check the md5 sum provided on the download site
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ENV MINICONDA_VERSION 4.5.11
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RUN cd /tmp && \
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wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
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echo "e1045ee415162f944b6aebfe560b8fee *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
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/bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
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rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
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$CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \
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$CONDA_DIR/bin/conda config --system --set auto_update_conda false && \
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$CONDA_DIR/bin/conda config --system --set show_channel_urls true && \
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$CONDA_DIR/bin/conda install --quiet --yes conda="${MINICONDA_VERSION%.*}.*" && \
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$CONDA_DIR/bin/conda update --all --quiet --yes && \
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conda clean -tipsy && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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USER root
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RUN ln -s /usr/bin/python3 /usr/bin/python && \
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mkdir /.symlinks && \
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cd /.symlinks &&
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ln -s $CONDA_DIR/conda conda && \
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ln -s $CONDA_DIR/activate activate && \
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ln -s $CONDA_DIR/deactivate deactivate && \
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export PATH=/.symlinks:$PATH
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USER $NB_UID
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# Install Tini
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RUN conda install --quiet --yes 'tini=0.18.0' && \
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conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
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conda clean -tipsy && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# Install Jupyter Notebook, Lab, and Hub
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# Generate a notebook server config
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# Cleanup temporary files
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# Correct permissions
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# Do all this in a single RUN command to avoid duplicating all of the
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# files across image layers when the permissions change
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RUN conda install --quiet --yes \
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'notebook=5.7.2' \
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'jupyterhub=0.9.4' \
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'jupyterlab=0.35.4' && \
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conda clean -tipsy && \
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jupyter labextension install @jupyterlab/hub-extension@^0.12.0 && \
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npm cache clean --force && \
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jupyter notebook --generate-config && \
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rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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USER root
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EXPOSE 8888
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WORKDIR $HOME
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# Configure container startup
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ENTRYPOINT ["tini", "-g", "--"]
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CMD ["start-notebook.sh"]
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### Minimal Notebook:
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USER root
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# Install all OS dependencies for fully functional notebook server
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RUN apt-get update && apt-get install -yq --no-install-recommends \
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build-essential \
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emacs \
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git \
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inkscape \
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jed \
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libsm6 \
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libxext-dev \
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libxrender1 \
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lmodern \
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netcat \
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pandoc \
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python-dev \
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texlive-fonts-extra \
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texlive-fonts-recommended \
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texlive-generic-recommended \
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texlive-latex-base \
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texlive-latex-extra \
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texlive-xetex \
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unzip \
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nano \
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&& rm -rf /var/lib/apt/lists/*
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### Now onto scipy-notebook
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# ffmpeg for matplotlib anim
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RUN apt-get update && \
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apt-get install -y --no-install-recommends ffmpeg && \
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rm -rf /var/lib/apt/lists/*
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USER $NB_UID
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# Install Python 3 packages
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# Remove pyqt and qt pulled in for matplotlib since we're only ever going to
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# use notebook-friendly backends in these images
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RUN conda install --quiet --yes \
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'conda-forge::blas=*=openblas' \
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'ipywidgets=7.2*' \
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'pandas=0.23*' \
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'numexpr=2.6*' \
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'matplotlib=2.2*' \
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'scipy=1.1*' \
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'seaborn=0.9*' \
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'scikit-learn=0.20*' \
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'scikit-image=0.14*' \
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'sympy=1.1*' \
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'cython=0.28*' \
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'patsy=0.5*' \
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'statsmodels=0.9*' \
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'cloudpickle=0.5*' \
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'dill=0.2*' \
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'numba=0.38*' \
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'bokeh=0.13*' \
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'sqlalchemy=1.2*' \
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'hdf5=1.10*' \
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'h5py=2.7*' \
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'vincent=0.4.*' \
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'beautifulsoup4=4.6.*' \
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'protobuf=3.*' \
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'xlrd' && \
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conda remove --quiet --yes --force qt pyqt && \
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conda clean -tipsy && \
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# Activate ipywidgets extension in the environment that runs the notebook server
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jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
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# Also activate ipywidgets extension for JupyterLab
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# Check this URL for most recent compatibilities
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# https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
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jupyter labextension install @jupyter-widgets/jupyterlab-manager@^0.38.1 && \
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jupyter labextension install jupyterlab_bokeh@0.6.3 && \
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npm cache clean --force && \
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rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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rm -rf /home/$NB_USER/.node-gyp && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# Install facets which does not have a pip or conda package at the moment
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RUN cd /tmp && \
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git clone https://github.com/PAIR-code/facets.git && \
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cd facets && \
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jupyter nbextension install facets-dist/ --sys-prefix && \
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cd && \
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rm -rf /tmp/facets && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# Import matplotlib the first time to build the font cache.
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ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
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RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
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fix-permissions /home/$NB_USER
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USER $NB_UID
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# Add local files as late as possible to avoid cache busting
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COPY start.sh /usr/local/bin/
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COPY start-notebook.sh /usr/local/bin/
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COPY start-singleuser.sh /usr/local/bin/
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COPY jupyter_notebook_config.py /etc/jupyter/
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RUN fix-permissions /etc/jupyter/
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31
singleuser/Dockerfile-R
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31
singleuser/Dockerfile-R
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@ -0,0 +1,31 @@
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FROM jupyter/r-notebook
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USER root
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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libapparmor1 \
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libedit2 \
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lsb-release \
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psmisc \
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libssl1.0.0 \
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;
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# You can use rsession from rstudio's desktop package as well.
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ENV RSTUDIO_PKG=rstudio-server-1.0.136-amd64.deb
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RUN wget -q http://download2.rstudio.org/${RSTUDIO_PKG}
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RUN dpkg -i ${RSTUDIO_PKG}
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RUN rm ${RSTUDIO_PKG}
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RUN conda install -c r r-shiny
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RUN apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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USER $NB_USER
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RUN pip install git+https://github.com/jupyterhub/jupyter-rsession-proxy
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# The desktop package uses /usr/lib/rstudio/bin
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ENV PATH="${PATH}:/usr/lib/rstudio-server/bin"
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ENV LD_LIBRARY_PATH="/usr/lib/R/lib:/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/opt/conda/lib/R/lib"
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