Dockerfile

# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.

# Ubuntu 18.04 (bionic) from 2018-04-26
# https://github.com/docker-library/official-images/commit/aac6a45b9eb2bffb8102353c350d341a410fb169
FROM ubuntu:bionic-20180426@sha256:c8c275751219dadad8fa56b3ac41ca6cb22219ff117ca98fe82b42f24e1ba64e

LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"

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 \
    curl \
    ncbi-blast+ \
 && apt-get clean \
 && rm -rf /var/lib/apt/lists/*

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

# Install Tini
RUN wget --quiet https://github.com/krallin/tini/releases/download/v0.18.0/tini && \
    echo "12d20136605531b09a2c2dac02ccee85e1b874eb322ef6baf7561cd93f93c855 *tini" | sha256sum -c - && \
    mv tini /usr/local/bin/tini && \
    chmod +x /usr/local/bin/tini

# Configure environment
ENV CONDA_DIR=/opt/conda \
    SHELL=/bin/bash \
    NB_USER=jovyan \
    NB_UID=1000 \
    NB_GID=100 \
    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 fix-permissions /usr/local/bin/fix-permissions
# Create jovyan user with UID=1000 and in the 'users' group
# and make sure these dirs are writable by the `users` group.
RUN groupadd wheel -g 11 && \
    echo "auth required pam_wheel.so use_uid" >> /etc/pam.d/su && \
    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

# 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
ENV MINICONDA_VERSION 4.5.1
RUN cd /tmp && \
    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
    echo "0c28787e3126238df24c5d4858bd0744 *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
    /bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
    rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
    $CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \
    $CONDA_DIR/bin/conda config --system --set auto_update_conda false && \
    $CONDA_DIR/bin/conda config --system --set show_channel_urls true && \
    $CONDA_DIR/bin/conda install --quiet --yes conda=4.5.4 && \
    $CONDA_DIR/bin/conda update --all --quiet --yes && \
    conda clean -tipsy && \
    rm -rf /home/$NB_USER/.cache/yarn && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

# Install Jupyter Notebook and Hub
RUN conda install --quiet --yes \
    'notebook=5.4.*' \
    'jupyterhub=0.8.*' \
    'jupyterlab=0.32.*' && \
    conda clean -tipsy && \
    jupyter labextension install @jupyterlab/hub-extension@^0.8.1 && \
    npm cache clean --force && \
    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
    rm -rf /home/$NB_USER/.cache/yarn && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

USER root

EXPOSE 8888
WORKDIR $HOME

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

# Add local files as late as possible to avoid cache busting
COPY start.sh /usr/local/bin/
COPY start-notebook.sh /usr/local/bin/
COPY start-singleuser.sh /usr/local/bin/
COPY jupyter_notebook_config.py /etc/jupyter/
COPY Blast-Tutorial.ipynb /home/jovyan/work
RUN fix-permissions /etc/jupyter/

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