Files to use as a base.
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FROM d4science/r-full:latest
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LABEL org.d4science.image.licenses="EUPL-1.2" \
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org.d4science.image.source="https://code-repo.d4science.org/gCubeSystem/rstudio-base" \
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org.d4science.image.vendor="D4Science <https://www.d4science.org>" \
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org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>, Roberto Cirillo <roberto.cirillo@isti.cnr.it>"
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ENV DEBIAN_FRONTEND=noninteractive
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ENV S6_VERSION=v2.1.0.2
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ENV RSTUDIO_VERSION=2023.03.0+386
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ENV DEFAULT_USER=rstudio
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ENV PANDOC_VERSION=default
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ENV QUARTO_VERSION=default
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ARG NB_USER="jovyan"
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ARG NB_UID="1000"
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ARG NB_GID="100"
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ARG HOME="/home/${NB_USER}"
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ENV S6_VERSION=v2.1.0.2
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ENV RSTUDIO_VERSION=2022.02.1+461
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ENV DEFAULT_USER="jovyan"
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ENV USERID="1000"
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ENV GROUPID="100"
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ENV PATH=/usr/lib/rstudio-server/bin:$PATH
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ENV R_HOME=/usr/local/lib/R
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# Configure environment
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ENV SHELL=/bin/bash \
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NB_USER="${NB_USER}" \
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NB_UID=${NB_UID} \
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NB_GID=${NB_GID} \
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LC_ALL=en_US.UTF-8 \
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LANG=en_US.UTF-8 \
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LANGUAGE=en_US.UTF-8
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ENV HOME="/home/${NB_USER}"
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RUN apt-get update --yes
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RUN /rocker_scripts/install_rstudio.sh
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RUN /rocker_scripts/install_pandoc.sh
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RUN /rocker_scripts/install_quarto.sh
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# This part comes from https://github.com/openanalytics/shinyproxy-rstudio-ide-demo/blob/master/Dockerfile
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RUN echo "www-frame-origin=same" >> /etc/rstudio/disable_auth_rserver.conf
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RUN echo "www-verify-user-agent=0" >> /etc/rstudio/disable_auth_rserver.conf
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RUN mv -f /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
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RUN echo "USER=$NB_USER" >> /etc/environment
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COPY rsession.conf /etc/rstudio/rsession.conf
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RUN chmod 0644 /etc/rstudio/rsession.conf
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RUN curl -o "${R_HOME}/etc/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"
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# Copy a script that we will use to correct permissions after running certain commands
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COPY fix-permissions /usr/local/bin/fix-permissions
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RUN chmod a+rx /usr/local/bin/fix-permissions
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# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
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# and make sure these dirs are writable by the `users` group.
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RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
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sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
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sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
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userdel -r "${NB_USER}" && \
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useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && \
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chmod g+w /etc/passwd && \
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fix-permissions "${HOME}"
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# Install the jupiterhub proxy
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RUN pip3 install \
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jsonschema'[format,format-nongpl]' \
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jupyterhub \
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jupyterlab \
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jupyter-rsession-proxy \
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jupyter-server-proxy \
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notebook
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RUN apt-get clean && rm -rf /var/lib/apt/lists/* && \
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echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
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locale-gen
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# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
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# hadolint ignore=SC2016
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RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc
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WORKDIR ${HOME}
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// REMEMBER TO FILL THE environment section with your values.
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// the following filed should be filled: imagename, git_url
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// REMEMBER to put your Dockerfile in the root folder of your project
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// The related jenkinsjob template is here:
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pipeline {
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agent {
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label 'docker'
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}
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environment {
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imagename = "d4science/rstudio-base"
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registryCredential = 'e348bfab-5580-4db6-b0e0-d854966bde08'
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dockerImage = ''
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git_url='https://code-repo.d4science.org/gCubeSystem/rstudio-base.git'
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}
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stages {
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stage('Cloning Git') {
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steps {
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git([url: git_url, branch: 'master', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346'])
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}
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}
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stage('Building image') {
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steps{
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script {
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dockerImage = docker.build imagename
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}
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}
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}
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stage('Deploy Image') {
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steps{
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script {
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docker.withRegistry( '', registryCredential ) {
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dockerImage.push("$BUILD_NUMBER")
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dockerImage.push('latest')
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}
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}
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}
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}
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stage('Remove Unused docker image') {
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steps{
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sh "docker rmi $imagename:$BUILD_NUMBER"
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sh "docker rmi $imagename:latest"
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}
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}
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}
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// post-build actions
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post {
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success {
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echo 'The docker pipeline worked!'
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emailext to: 'jenkinsbuilds@d4science.org',
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subject: "[Jenkins DockerPipeline D4S] build ${currentBuild.fullDisplayName} worked",
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body: "Build time: ${currentBuild.durationString}. See ${env.BUILD_URL}"
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}
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failure {
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echo 'The docker pipeline has failed'
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emailext attachLog: true,
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to: 'jenkinsbuilds@d4science.org',
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subject: "[Jenkins DockerPipeline D4S] build ${currentBuild.fullDisplayName} failed for image ${imagename}",
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body: "Something is wrong with ${env.BUILD_URL}"
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}
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}
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}
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# rstudio-base
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# rstudio-base
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Rstudio image that builds from "r-full"
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Rstudio image that builds from "r-full"
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* One branch for each corresponding *major.minor* `R` version
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* Customizations will be done in rstudio-custom-X
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#!/bin/bash
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# From https://github.com/jupyter/docker-stacks/blob/main/docker-stacks-foundation/fix-permissions
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# set permissions on a directory
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# after any installation, if a directory needs to be (human) user-writable,
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# run this script on it.
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# It will make everything in the directory owned by the group ${NB_GID}
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# and writable by that group.
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# Deployments that want to set a specific user id can preserve permissions
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# by adding the `--group-add users` line to `docker run`.
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# uses find to avoid touching files that already have the right permissions,
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# which would cause massive image explosion
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# right permissions are:
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# group=${NB_GID}
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# AND permissions include group rwX (directory-execute)
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# AND directories have setuid,setgid bits set
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set -e
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for d in "$@"; do
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find "${d}" \
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! \( \
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-group "${NB_GID}" \
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-a -perm -g+rwX \
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\) \
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-exec chgrp "${NB_GID}" -- {} \+ \
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-exec chmod g+rwX -- {} \+
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# setuid, setgid *on directories only*
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find "${d}" \
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\( \
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-type d \
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-a ! -perm -6000 \
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\) \
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-exec chmod +6000 -- {} \+
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done
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session-timeout-minutes=7200
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session-disconnected-timeout-minutes=1440
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session-quit-child-processes-on-exit=0
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session-default-working-dir=~
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session-default-new-project-dir=~
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# session-save-action-default=yes
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allow-shell=1
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#allow-terminal-websockets=1
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limit-cpu-time-minutes=0
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limit-file-upload-size-mb=0
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#limit-xfs-disk-quota=no
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