Dockerfile

FROM nvidia/cuda:10.1-cudnn7-runtime-ubuntu18.04

### Start jupyter/base-notebook
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
#ARG NB_USER="jovyan"
ARG NB_USER="dspuser"
ARG NB_UID="1000"
ARG NB_GID="100"

USER root

# Install all OS dependencies for notebook server that starts but lacks all
# features (e.g., download as all possible file formats)
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update && apt-get -yq dist-upgrade \
 && apt-get install -yq --no-install-recommends \
    wget \
    bzip2 \
    ca-certificates \
    sudo \
    locales \
    fonts-liberation \
    run-one \
 && rm -rf /var/lib/apt/lists/*

RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
    locale-gen

# Configure environment
ENV CONDA_DIR=/opt/conda \
    SHELL=/bin/bash \
    NB_USER=$NB_USER \
    NB_UID=$NB_UID \
    NB_GID=$NB_GID \
    LC_ALL=en_US.UTF-8 \
    LANG=en_US.UTF-8 \
    LANGUAGE=en_US.UTF-8
ENV PATH=$CONDA_DIR/bin:$PATH \
    HOME=/home/$NB_USER

# Add a script that we will use to correct permissions after running certain commands
ADD bin/fix-permissions /usr/local/bin/fix-permissions

#Edit to original to make fix-permission executable
RUN chmod +x /usr/local/bin/fix-permissions

# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc

# Create NB_USER wtih name jovyan user with UID=1000 and in the 'users' group
# and make sure these dirs are writable by the `users` group.
RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
    sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
    sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
    useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
    mkdir -p $CONDA_DIR && \
    chown $NB_USER:$NB_GID $CONDA_DIR && \
    chmod g+w /etc/passwd && \
    fix-permissions $HOME && \
    fix-permissions $CONDA_DIR

USER $NB_UID
WORKDIR $HOME
ARG PYTHON_VERSION=default

# Setup work directory for backward-compatibility
RUN mkdir /home/$NB_USER/work && \
    fix-permissions /home/$NB_USER

# Install conda as jovyan and check the md5 sum provided on the download site
# Install conda as jovyan and check the md5 sum provided on the download site
ENV MINICONDA_VERSION=4.8.2 \
    MINICONDA_MD5=87e77f097f6ebb5127c77662dfc3165e \
    CONDA_VERSION=4.8.2

WORKDIR /tmp
RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh && \
    echo "${MINICONDA_MD5} *Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
    /bin/bash Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
    rm Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh && \
    echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
    conda config --system --prepend channels conda-forge && \
    conda config --system --set auto_update_conda false && \
    conda config --system --set show_channel_urls true && \
    conda config --system --set channel_priority strict && \
    if [ ! $PYTHON_VERSION = 'default' ]; then conda install --yes python=$PYTHON_VERSION; fi && \
    conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \
    conda install --quiet --yes conda && \
    conda install --quiet --yes pip && \
    conda update --all --quiet --yes && \
    conda clean --all -f -y && \
    rm -rf /home/$NB_USER/.cache/yarn && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

# Install Tini
RUN conda install --quiet --yes 'tini=0.18.0' && \
    conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
    conda clean --all -f -y && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

# Install Jupyter Notebook, Lab, and Hub
# Generate a notebook server config
# Cleanup temporary files
# Correct permissions
# Do all this in a single RUN command to avoid duplicating all of the
# files across image layers when the permissions change
RUN conda install --quiet --yes \
    'notebook=6.0.3' \
    'jupyterhub=1.1.0' \
    'jupyterlab=2.1.3' && \
    conda clean --all -f -y && \
    npm cache clean --force && \
    jupyter notebook --generate-config && \
    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
    rm -rf /home/$NB_USER/.cache/yarn && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

### End jupyter/base-notebook

### Start jupyter/minimal-notebook
USER root

# Install all OS dependencies for fully functional notebook server
RUN apt-get update && apt-get install -yq --no-install-recommends \
    build-essential \
    emacs-nox \
    vim-tiny \
    git \
    inkscape \
    jed \
    libsm6 \
    libxext-dev \
    libxrender1 \
    lmodern \
    netcat \
    python-dev \
    # ---- nbconvert dependencies ----
    texlive-xetex \
    texlive-fonts-recommended \
    texlive-plain-generic \
    # Optional dependency
    texlive-fonts-extra \
    # ----
    tzdata \
    unzip \
    nano \
    && apt-get clean && rm -rf /var/lib/apt/lists/*

# Switch back to jovyan to avoid accidental container runs as root
USER $NB_UID
### End jupyter/minimal-notebook

# R packages including IRKernel which gets installed globally.
RUN conda install --quiet --yes \
    'r-base=3.6.3' \
    'r-caret=6.0*' \
    'r-crayon=1.3*' \
    'r-devtools=2.3*' \
    'r-forecast=8.12*' \
    'r-hexbin=1.28*' \
    'r-htmltools=0.4*' \
    'r-htmlwidgets=1.5*' \
    'r-irkernel=1.1*' \
    'r-plyr=1.8*' \
    'r-randomforest=4.6*' \
    'r-rcurl=1.98*' \
    'r-reshape2=1.4*' \
    'r-rmarkdown=2.1*' \
    'r-rsqlite=2.2*' \
    'r-shiny=1.4*' \
    'r-tidyverse=1.3*' \
    'rpy2=3.1*' \
    && \
    conda clean --all -f -y && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

WORKDIR $HOME

### End jupyter/datascience-notebook

### Install RStudio Server and supporting proxy
# You can use rsession from rstudio's desktop package as well.

USER root 

RUN apt-get update && \
        apt-get install -y --no-install-recommends \
                libapparmor1 \
                libedit2 \
                lsb-release \
                psmisc \
                libssl1.0.0 \
                libclang-dev \
                ;

ENV RSTUDIO_PKG=rstudio-server-1.3.959-amd64.deb

RUN wget -q http://download2.rstudio.org/server/bionic/amd64/${RSTUDIO_PKG}
RUN dpkg -i ${RSTUDIO_PKG}
RUN rm ${RSTUDIO_PKG}

RUN apt-get clean && \
    rm -rf /var/lib/apt/lists/*


USER $NB_USER

RUN pip install git+https://github.com/jupyterhub/jupyter-rsession-proxy

RUN cd /tmp/ && \
    git clone --depth 1 https://github.com/jupyterhub/jupyter-server-proxy && \
    cd jupyter-server-proxy/jupyterlab-server-proxy && \
    npm install && npm run build && jupyter labextension link . && \
    npm run build && jupyter lab build

# The desktop package uses /usr/lib/rstudio/bin
ENV PATH="${PATH}:/usr/lib/rstudio-server/bin"
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"

### End install RStudio Server

### Install jupyterlab-git extension
### Might need to conda pip install from git to get latest version
#RUN conda install -c conda-forge jupyterlab-git && \
    #jupyter lab build
RUN pip install git+https://github.com/jupyterlab/jupyterlab-git && \
    jupyter lab build
### End install jupyterlab-git

EXPOSE 8888

# Configure container startup
ENTRYPOINT ["tini", "-g", "--"]
CMD ["start-notebook.sh"]

# Add local files as late as possible to avoid cache busting
COPY bin/start.sh /usr/local/bin/
COPY bin/start-notebook.sh /usr/local/bin/
COPY bin/start-singleuser.sh /usr/local/bin/
COPY config/jupyter_notebook_config.py /etc/jupyter/

# Fix permissions on /etc/jupyter as root
USER root
RUN fix-permissions /etc/jupyter/

# Fix permissions on /etc/jupyter as root
USER root
RUN chmod +x /usr/local/bin/start-notebook.sh
RUN fix-permissions /etc/jupyter/

# 7 JULY 2020 Additions - Added here to stop cache busting
RUN apt-get update && \
        apt-get install -y --no-install-recommends \
                curl

COPY environment.yml .

RUN conda create --quiet --yes --name r2d --file environment.yml

##### Try to keep you changes in this block

#Adding extra system packages
#RUN apt-get update && \
#       apt-get install -y --no-install-recommends \
#                package-name1 \
#                package-name2 \
#                package-name2 && \
#       && apt-get clean && rm -rf /var/lib/apt/lists/*

#Cloning a repository to your HOME directory
#RUN git clone https://github.com/wp-cdas/ExampleRepo $HOME/new-folder-name

#Copying a file from the top folder of the repo 
# (with the Dockerfile, etc) to your HOME directory
#COPY filename $HOME

#####

# Switch back to jovyan to avoid accidental container runs as root
USER $NB_UID

WORKDIR $HOME