generated from gCubeCI/Pipeline-Docker-Template
110 lines
4.4 KiB
Docker
110 lines
4.4 KiB
Docker
FROM d4science/r-studio-requirement
|
|
|
|
LABEL org.d4science.image.licenses="EUPL-1.2" \
|
|
org.d4science.image.source="https://code-repo.d4science.org/gCubeSystem/r-studio-requirement" \
|
|
org.d4science.image.vendor="D4Science <https://www.d4science.org>" \
|
|
org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>, Roberto Cirillo <roberto.cirillo@isti.cnr.it>" \
|
|
org.d4science.image.r_version="2022.02.1+461"
|
|
|
|
ARG NB_USER="jovyan"
|
|
ARG NB_UID="1000"
|
|
ARG NB_GID="100"
|
|
ARG HOME="/home/${NB_USER}"
|
|
ENV S6_VERSION=v2.1.0.2
|
|
ENV RSTUDIO_VERSION=2022.02.1+461
|
|
ENV DEFAULT_USER="jovyan"
|
|
ENV USERID="1000"
|
|
ENV GROUPID="100"
|
|
ENV PANDOC_VERSION=default
|
|
ENV PATH=/usr/lib/rstudio-server/bin:$PATH
|
|
ENV DEBIAN_FRONTEND=noninteractive
|
|
ENV R_HOME=/usr/local/lib/R
|
|
# Configure environment
|
|
ENV SHELL=/bin/bash \
|
|
NB_USER="${NB_USER}" \
|
|
NB_UID=${NB_UID} \
|
|
NB_GID=${NB_GID} \
|
|
LC_ALL=en_US.UTF-8 \
|
|
LANG=en_US.UTF-8 \
|
|
LANGUAGE=en_US.UTF-8
|
|
ENV HOME="/home/${NB_USER}"
|
|
|
|
RUN apt-get update --yes && \
|
|
apt-get upgrade --yes && \
|
|
apt-get install --yes --no-install-recommends \
|
|
python3 python3-pip \
|
|
curl
|
|
RUN /rocker_scripts/install_rstudio.sh
|
|
|
|
# This part comes from https://github.com/openanalytics/shinyproxy-rstudio-ide-demo/blob/master/Dockerfile
|
|
RUN echo "www-frame-origin=same" >> /etc/rstudio/disable_auth_rserver.conf
|
|
RUN echo "www-verify-user-agent=0" >> /etc/rstudio/disable_auth_rserver.conf
|
|
|
|
# The 0*_ scripts cannot be used anymore at startup time
|
|
|
|
COPY 01_set_env.sh /root/01_set_env.sh
|
|
RUN chmod a+rx /root/01_set_env.sh
|
|
RUN /root/01_set_env.sh
|
|
|
|
# ADD 02_userconf.sh /etc/cont-init.d/02_userconf
|
|
RUN mv -f /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
|
|
RUN echo "USER=$NB_USER" >> /etc/environment
|
|
|
|
# ADD 03_setup_root_path.sh /etc/cont-init.d/03_setup_root_path
|
|
# ADD 05_setup_rsession_parameters.sh /etc/cont-init.d/05_setup_rsession_parameters
|
|
RUN echo "session-timeout-minutes=7200" >> /etc/rstudio/rsession.conf
|
|
RUN echo "session-disconnected-timeout-minutes=1440" >> /etc/rstudio/rsession.conf
|
|
RUN echo "session-quit-child-processes-on-exit=0" >> /etc/rstudio/rsession.conf
|
|
RUN echo "session-default-working-dir=~" >> /etc/rstudio/rsession.conf
|
|
RUN echo "session-default-new-project-dir=~" >> /etc/rstudio/rsession.conf
|
|
RUN #echo "session-save-action-default=yes" >> /etc/rstudio/rsession.conf
|
|
RUN echo "allow-shell=1" >> /etc/rstudio/rsession.conf
|
|
RUN #echo "allow-terminal-websockets=1" >> /etc/rstudio/rsession.conf
|
|
RUN echo "limit-cpu-time-minutes=0" >> /etc/rstudio/rsession.conf
|
|
RUN echo "limit-file-upload-size-mb=0" >> /etc/rstudio/rsession.conf
|
|
RUN #echo "limit-xfs-disk-quota=no" >> /etc/rstudio/rsession.conf
|
|
RUN curl -o "${R_HOME}/etc/R/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"
|
|
|
|
# Copy a script that we will use to correct permissions after running certain commands
|
|
COPY fix-permissions /usr/local/bin/fix-permissions
|
|
RUN chmod a+rx /usr/local/bin/fix-permissions
|
|
|
|
# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
|
|
# and make sure these dirs are writable by the `users` group.
|
|
RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
|
|
sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
|
|
sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
|
|
userdel -r "${NB_USER}" && \
|
|
useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && \
|
|
chmod g+w /etc/passwd && \
|
|
fix-permissions "${HOME}"
|
|
|
|
# Install the jupiterhub proxy
|
|
RUN pip3 install \
|
|
jsonschema'[format,format-nongpl]' \
|
|
jupyterhub \
|
|
jupyterlab \
|
|
jupyter-rsession-proxy \
|
|
jupyter-server-proxy \
|
|
notebook
|
|
|
|
RUN apt-get clean && rm -rf /var/lib/apt/lists/* && \
|
|
echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
|
|
locale-gen
|
|
|
|
# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
|
|
# hadolint ignore=SC2016
|
|
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc
|
|
|
|
WORKDIR ${HOME}
|
|
|
|
# Prepare the workspace environment
|
|
# RUN mkdir -p /opt/workspace-lib
|
|
# RUN mkdir /var/log/workspace-lib
|
|
# ADD https://maven.d4science.org/nexus/content/repositories/gcube-snapshots/org/gcube/data-access/sh-fuse-integration/2.0.0-SNAPSHOT/sh-fuse-integration-2.0.0-20211005.090627-1-jar-with-dependencies.jar /opt/workspace-lib/fuse-workspace.jar
|
|
# ADD 06_workspace_mount.sh /etc/cont-init.d/06_workspace_mount
|
|
# ADD 06-fuse-logback.xml /opt/workspace-lib/logback.xml
|
|
|
|
# EXPOSE 8787
|
|
# CMD ["/init"]
|