feat: adding a bioconductor base (#67)

Makefile

@@ -17,7 +17,7 @@
 # limitations under the License.
 
 extensions = \
-	r \
+	r-bioconductor_3_10 r \
 	cuda-9.2 cuda-10.0-tensorflow-1.14
 
 DOCKER_PREFIX?=renku/singleuser

docker/base/Dockerfile

@@ -62,7 +62,7 @@ RUN conda install gxx_linux-64
 ENV RENKU_DISABLE_VERSION_CHECK 1
 
 RUN python3 -m pip install pipx>=0.15.0.0
-ARG RENKU_PIP_SPEC=""
+ARG RENKU_PIP_SPEC="renku"
 RUN pipx install ${RENKU_PIP_SPEC} --pip-args="--pre" && \
     pipx inject renku sentry-sdk && \
     pipx ensurepath

docker/r-bioconductor_3_10/Dockerfile

@@ -0,0 +1,117 @@
+ARG RELEASE=RELEASE_3_10
+FROM bioconductor/bioconductor_docker:${RELEASE}
+LABEL maintainer="Swiss Data Science Center <[email protected]>"
+
+USER root
+
+ENV NB_USER rstudio
+ENV NB_UID 1000
+ENV NB_GID 1000
+ENV VENV_DIR /srv/venv
+ENV HOME /home/${NB_USER}
+ENV SHELL bash
+ENV CONDA_PATH /opt/conda
+
+# prepend conda to PATH
+ENV PATH ${CONDA_PATH}/bin:$PATH
+# And set PATH for R! It doesn't read from the environment...
+RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \
+    echo "PATH=${PATH}" >> /etc/profile.d/set_path.sh
+
+# The `rsession` binary that is called by nbrsessionproxy to start R doesn't seem to start
+# without this being explicitly set
+ENV LD_LIBRARY_PATH /usr/local/lib/R/lib
+
+# Add Tini
+ENV TINI_VERSION v0.18.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini
+
+# install miniconda (https://github.com/ContinuumIO/docker-images/blob/master/miniconda3/debian/Dockerfile)
+RUN apt-get update --fix-missing && \
+    apt-get install -yq --no-install-recommends \
+        bzip2 \
+        ca-certificates \
+        curl \
+        gnupg \
+        libglib2.0-0 \
+        libsm6 \
+        libxext6 \
+        libxrender1 \
+        wget \
+        vim && \
+    apt-get purge && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# install git-lfs
+RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | sudo bash && \
+    apt-get install git-lfs
+
+WORKDIR /tmp
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p ${CONDA_PATH} && \
+    rm ~/miniconda.sh && \
+    ${CONDA_PATH}/bin/conda clean -tipsy && \
+    ln -s ${CONDA_PATH}/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    ${CONDA_PATH}/bin/conda config --system --append channels conda-forge && \
+    ${CONDA_PATH}/bin/conda config --system --set auto_update_conda false && \
+    find ${CONDA_PATH}/ -follow -type f -name '*.a' -delete && \
+    find ${CONDA_PATH}/ -follow -type f -name '*.js.map' -delete && \
+    ${CONDA_PATH}/bin/conda clean -afy
+
+# set permissions in the conda directory to be editable by NB_USER
+ADD fix-permissions.sh /usr/local/bin
+RUN fix-permissions.sh ${CONDA_PATH}
+
+USER ${NB_USER}
+
+# set up conda in the NB_USER environment
+RUN echo ". ${CONDA_PATH}/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
+
+# install the jupyter stack
+ARG JUPYTERHUB_VERSION=0.9.6
+
+RUN ${CONDA_PATH}/bin/conda install --quiet --yes \
+    'notebook=6.0.0' \
+    "jupyterhub=${JUPYTERHUB_VERSION}" \
+    'jupyterlab=1.2.1' && \
+    ${CONDA_PATH}/bin/conda install -c conda-forge 'nodejs>=6.11.5' && \
+    ${CONDA_PATH}/bin/conda install --quiet --yes conda-build && \
+    ${CONDA_PATH}/bin/conda build purge-all && \
+    npm cache clean --force
+
+RUN jupyter notebook --generate-config && \
+    rm -rf ${CONDA_PATH}/share/jupyter/lab/staging && \
+    rm -rf /home/$NB_USER/.cache/yarn && \
+    pip install -U --no-cache-dir pip wheel
+
+
+# install jupyterlab, git extension
+RUN python3 -m pip install -U pip && \
+    jupyter labextension update @jupyterlab/hub-extension --no-build && \
+    jupyter labextension install @jupyterlab/git --no-build && \
+    jupyter labextension list && \
+    pip install jupyter-rsession-proxy && \
+    pip install jupyterlab-git && \
+    jupyter serverextension enable --py jupyterlab_git && \
+    jupyter lab build
+
+# install IRKernel
+RUN R --quiet -e "install.packages('IRkernel')" && \
+    R --quiet -e "IRkernel::installspec(prefix='${CONDA_PATH}')"
+
+# install renku
+# the RENKU_PIP_SPEC should be e.g. "renku==0.5.2"
+ARG RENKU_PIP_SPEC="renku"
+RUN python3 -m pip install pipx>=0.15.0.0 && \
+    pipx install ${RENKU_PIP_SPEC} --pip-args="--pre" && \
+    pipx inject renku sentry-sdk && \
+    pipx ensurepath
+
+COPY entrypoint.sh /entrypoint.sh
+ENTRYPOINT [ "/tini", "--", "/entrypoint.sh" ]
+CMD [ "jupyterhub-singleuser" ]
+
+WORKDIR ${HOME}

docker/r-bioconductor_3_10/LICENSE-fix-permissions

@@ -0,0 +1,60 @@
+# Licensing terms
+
+`fix-permissions.sh` is licensed under the terms of the Modified BSD License
+(also known as New or Revised or 3-Clause BSD), as follows:
+
+- Copyright (c) 2001-2015, IPython Development Team
+- Copyright (c) 2015-, Jupyter Development Team
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+Redistributions in binary form must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+Neither the name of the Jupyter Development Team nor the names of its
+contributors may be used to endorse or promote products derived from this
+software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+## About the Jupyter Development Team
+
+The Jupyter Development Team is the set of all contributors to the Jupyter project.
+This includes all of the Jupyter subprojects.
+
+The core team that coordinates development on GitHub can be found here:
+https://github.com/jupyter/.
+
+## Our Copyright Policy
+
+Jupyter uses a shared copyright model. Each contributor maintains copyright
+over their contributions to Jupyter. But, it is important to note that these
+contributions are typically only changes to the repositories. Thus, the Jupyter
+source code, in its entirety is not the copyright of any single person or
+institution.  Instead, it is the collective copyright of the entire Jupyter
+Development Team.  If individual contributors want to maintain a record of what
+changes/contributions they have specific copyright on, they should indicate
+their copyright in the commit message of the change, when they commit the
+change to one of the Jupyter repositories.
+
+With this in mind, the following banner should be used in any source code file
+to indicate the copyright and license terms:
+
+    # Copyright (c) Jupyter Development Team.
+    # Distributed under the terms of the Modified BSD License.

docker/r-bioconductor_3_10/entrypoint.sh

@@ -0,0 +1,59 @@
+#!/bin/bash
+
+# Copy the relevant system environment variables to the R-specific locations
+VariableArray=("GIT_COMMITTER_NAME"  "GIT_AUTHOR_NAME"  "EMAIL")
+for var in ${VariableArray[*]}; do
+    if [ -n "${!var}" ]; then
+        echo $var=${!var} >> ${HOME}/.Renviron
+    fi
+done
+
+# Setup git user
+if [ -z "$(git config --global --get user.name)" ]; then
+    git config --global user.name "$GIT_AUTHOR_NAME"
+fi
+if [ -z "$(git config --global --get user.email)" ]; then
+    git config --global user.email "$EMAIL"
+fi
+
+# add a symlink to the project directory in /home/rstudio
+[ -n "$CI_PROJECT" ] && ln -s /work/${CI_PROJECT} /home/rstudio
+
+# configure rstudio to open the rpath project
+if [[ ! -f /home/rstudio/${CI_PROJECT}/${CI_PROJECT}.Rproj ]]; then
+cat > /home/rstudio/${CI_PROJECT}/${CI_PROJECT}.Rproj <<- EOM
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+EOM
+fi
+mkdir -p /home/rstudio/.rstudio/projects_settings
+echo /home/rstudio/${CI_PROJECT}/${CI_PROJECT}.Rproj | tee /home/rstudio/.rstudio/projects_settings/next-session-project
+chown -R rstudio:root /home/rstudio/.rstudio/projects_settings
+
+#
+# copy the environment from renku-env repo
+#
+
+# clone the repo
+proto=$(echo $GITLAB_URL | sed -e's,^\(.*://\).*,\1,g')
+url=$(echo ${GITLAB_URL/$proto/})
+user=$(echo ${CI_REPOSITORY_URL/$proto/} | grep @ | cut -d@ -f1)
+
+git clone --depth 1 ${proto}${user}@${url}/${JUPYTERHUB_USER}/renku-env.git /tmp/renku-env || true
+
+# append the contents of all the files to same files in ${HOME}
+find /tmp/renku-env -not -path '*.git*' -type f -print0 | xargs --null -I{} sh -c 'cat {} >> ${HOME}/$(basename "{}")' || true
+
+# run the command
+$@

docker/r-bioconductor_3_10/fix-permissions.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+# set permissions on a directory
+# after any installation, if a directory needs to be (human) user-writable,
+# run this script on it.
+# It will make everything in the directory owned by the group $NB_GID
+# and writable by that group.
+# Deployments that want to set a specific user id can preserve permissions
+# by adding the `--group-add users` line to `docker run`.
+
+# uses find to avoid touching files that already have the right permissions,
+# which would cause massive image explosion
+
+# right permissions are:
+# group=$NB_GID
+# AND permissions include group rwX (directory-execute)
+# AND directories have setuid,setgid bits set
+
+set -e
+
+for d in "$@"; do
+  find "$d" \
+    ! \( \
+      -group $NB_GID \
+      -a -perm -g+rwX  \
+    \) \
+    -exec chgrp $NB_GID {} \; \
+    -exec chmod g+rwX {} \;
+  # setuid,setgid *on directories only*
+  find "$d" \
+    \( \
+        -type d \
+        -a ! -perm -6000  \
+    \) \
+    -exec chmod +6000 {} \;
+done

docker/r/Dockerfile

@@ -99,7 +99,7 @@ RUN R --quiet -e "install.packages('IRkernel')" && \
 
 # install renku
 # the RENKU_PIP_SPEC should be e.g. "renku==0.5.2"
-ARG RENKU_PIP_SPEC=""
+ARG RENKU_PIP_SPEC="renku"
 RUN python3 -m pip install pipx>=0.15.0.0 && \
     pipx install ${RENKU_PIP_SPEC} --pip-args="--pre" && \
     pipx inject renku sentry-sdk && \

docker/r/entrypoint.sh

@@ -19,6 +19,29 @@ fi
 # add a symlink to the project directory in /home/rstudio
 [ -n "$CI_PROJECT" ] && ln -s /work/${CI_PROJECT} /home/rstudio
 
+
+# configure rstudio to open the rpath project
+if [[ ! -f /home/rstudio/${CI_PROJECT}/${CI_PROJECT}.Rproj ]]; then
+cat > /home/rstudio/${CI_PROJECT}/${CI_PROJECT}.Rproj <<- EOM
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+EOM
+fi
+mkdir -p /home/rstudio/.rstudio/projects_settings 
+echo /home/rstudio/${CI_PROJECT}/${CI_PROJECT}.Rproj | tee /home/rstudio/.rstudio/projects_settings/next-session-project
+chown -R rstudio:root /home/rstudio/.rstudio/projects_settings
+
 #
 # copy the environment from renku-env repo
 #