Add support for R lang

Dockerfile

@@ -93,6 +93,9 @@ 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 && \

Dockerfile.with_r

@@ -0,0 +1,179 @@
+# 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 <[email protected]>"
+
+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 [email protected] [email protected] [email protected]
+
+# install R
+RUN apt-get update && apt-get install -yq r-base && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Install R packages
+RUN R -e "install.packages(c('tidyverse'), quiet = TRUE)"
+
+# Install rpy2
+RUN pip install rpy2
+
+# 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