Dockerfile

# Copyright (c) Reference Genomics, Inc.
# Distributed under the terms of the Modified BSD License.
# Extended from github.com/jupyter/docker-stacks
# See also http://blog.dscpl.com.au/2016/01/roundup-of-docker-issues-when-hosting.html

FROM python:3.8.3-slim-buster

LABEL maintainer="Nick Greenfield <nick@onecodex.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 install -yq --no-install-recommends \
    apt-transport-https \
    build-essential \
    bzip2 \
    ca-certificates \
    cmake \
    curl \
    fonts-dejavu \
    gcc \
    gfortran \
    git \
    gnupg \
    locales \
    python-dev \
    sudo \
    unzip \
    vim \
    wget \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

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

# Add Tini
ENV TINI_VERSION v0.18.0
ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/local/bin/tini
RUN chmod +x /usr/local/bin/tini \
    && echo "12d20136605531b09a2c2dac02ccee85e1b874eb322ef6baf7561cd93f93c855 /usr/local/bin/tini" | sha256sum -c -

# Configure environment
ENV SHELL /bin/bash
ENV NB_USER jovyan
ENV NB_UID 1000
ENV HOME /home/$NB_USER
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US.UTF-8
ENV PATH $HOME/.local/bin:$PATH

# Disable npm package update notifications (DEV-4202)
ENV NO_UPDATE_NOTIFIER=1

# Create jovyan user with UID=1000 and in the root group
# See https://github.com/jupyter/docker-stacks/issues/188
RUN useradd -m -s /bin/bash -N -u $NB_UID -g 0 $NB_USER

# Setup jovyan home directory
RUN mkdir /home/$NB_USER/work && \
    mkdir /home/$NB_USER/.jupyter && \
    mkdir -p -m 770 /home/$NB_USER/.local/share/jupyter && \
    echo "cacert=/etc/ssl/certs/ca-certificates.crt" > /home/$NB_USER/.curlrc

# Update pip
RUN pip install --upgrade pip

# Install awscli
# IMPORTANT: this is required for saving the notebook to S3
RUN pip install awscli==1.22.55

# Install numpy
RUN pip install numpy==1.18.4

# Install  bipython
RUN pip install biopython==1.78

# Install Jupyter extensions
RUN pip install ipywidgets jupyter_contrib_nbextensions

# Pin nbconvert to 5.x.x
RUN pip install nbconvert==5.6

# Install other helpful modules
RUN pip install openpyxl==3.0.3 xlrd==1.2.0 statsmodels==0.11.1

# Install weasyprint
RUN pip install WeasyPrint==51

# Jupyter notebook should have already been installed above, but here we force a particular version
RUN pip install onecodex[all,reports]==0.9.6

# Install taxonomy
RUN pip install taxonomy

# Activate ipywidgets extension in the environment that runs the notebook server
RUN jupyter nbextension enable --py widgetsnbextension --sys-prefix
RUN jupyter contrib nbextension install --user && \
    jupyter nbextension enable python-markdown/main

WORKDIR /home/$NB_USER/work

# Install nss_wrapper
RUN wget https://ftp.samba.org/pub/cwrap/nss_wrapper-1.1.2.tar.gz && \
    mkdir nss_wrapper && \
    tar -xC nss_wrapper --strip-components=1 -f nss_wrapper-1.1.2.tar.gz && \
    rm nss_wrapper-1.1.2.tar.gz && \
    mkdir nss_wrapper/obj && \
    (cd nss_wrapper/obj && \
    cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DLIB_SUFFIX=64 .. && \
    make && \
    make install) && \
    rm -rf nss_wrapper

# Dependencies for weasyprint. Known bugs on libcairo < 1.15.4. Must pull from debian-buster to get 1.16
RUN echo "deb http://deb.debian.org/debian buster main" >> /etc/apt/sources.list \
    && apt-get update \
    && apt-get install -yq --no-install-recommends \
    libffi6 \
    libcairo2 \
    libpango1.0.0 \
    fonts-texgyre \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

# Copy `onecodex` installed fonts to local directory
RUN cp /usr/local/lib/python3.8/site-packages/onecodex/assets/fonts/*.otf /usr/local/share/fonts && fc-cache

# Install Node and vega-cli for server-side image rendering
RUN curl -sL https://deb.nodesource.com/setup_14.x | bash -
RUN apt-get -y install nodejs
RUN npm install -g --unsafe-perm vega-cli@5.13.0 vega-lite@4.13.0 canvas@2.6.1

# Configure container startup
EXPOSE 8888
COPY notebook/entrypoint.sh /usr/local/bin/entrypoint.sh
RUN chmod +x /usr/local/bin/entrypoint.sh
ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
CMD ["jupyter", "notebook"]

# Add assets
RUN mkdir /opt/onecodex/
COPY notebook/notebook.html /usr/local/lib/python3.8/site-packages/notebook/templates
COPY notebook/override.css /usr/local/lib/python3.8/site-packages/notebook/static/notebook/css
COPY notebook/onecodex.js /home/$NB_USER/.jupyter/custom/
COPY notebook/one-codex-spinner.svg /home/$NB_USER/.jupyter/custom/

# Add local files
COPY notebook/jupyter_notebook_config.py /home/$NB_USER/.jupyter/
COPY notebook/token_notebook.py /usr/local/bin/token_notebook.py
COPY notebook/save_message_handler.js /usr/local/share/jupyter/customextensions/
RUN jupyter nbextension install /usr/local/share/jupyter/customextensions/ \
    && jupyter nbextension enable customextensions/save_message_handler
RUN chmod +x /usr/local/bin/token_notebook.py

# Add patch to jupyter notebook for export to One Codex document portal
COPY notebook/notebook.patch /usr/local/lib/python3.8/site-packages/notebook
RUN cd /usr/local/lib/python3.8/site-packages/notebook \
    && patch -p0 < notebook.patch

# Finally fix permissions on everything
# See https://github.com/jupyter/docker-stacks/issues/188
# RUN chown -R $NB_USER:root /home/$NB_USER && chmod -R u+rw,g+rw /home/$NB_USER
RUN chown -R $NB_USER:root /home/$NB_USER && find /home/$NB_USER -type d -exec chmod 775 {} \;

# Switch to unprivileged user, jovyan
USER $NB_USER