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FROM quay.io/jupyter/base-notebook:2025-02-03
# https://quay.io/repository/jupyter/base-notebook?tab=tags
LABEL maintainer="Neurodesk Project <www.neurodesk.org>"
USER root
#========================================#
# Core services
#========================================#
# Install base image dependencies
RUN apt-get update --yes \
&& DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends \
software-properties-common \
openjdk-21-jre \
build-essential \
libcairo2-dev \
libjpeg-turbo8-dev \
libpng-dev \
libtool-bin \
uuid-dev \
freerdp2-dev \
libvncserver-dev \
libssl-dev \
libwebp-dev \
libssh2-1-dev \
libpango1.0-dev \
tigervnc-common \
tigervnc-standalone-server \
tigervnc-tools \
xorgxrdp \
xrdp \
lxde \
acl \
wget \
curl \
dirmngr \
gpg \
gpg-agent \
apt-transport-https \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
# add a static strace executable to /opt which we can copy to containers for debugging:
RUN mkdir -p /opt/strace \
&& wget -qO- https://github.com/JuliaBinaryWrappers/strace_jll.jl/releases/download/strace-v6.7.0%2B1/strace.v6.7.0.x86_64-linux-gnu.tar.gz | tar xz -C /opt/strace --strip-components=1 \
&& chmod +x /opt/strace
ARG TOMCAT_REL="9"
ARG TOMCAT_VERSION="9.0.97"
ARG GUACAMOLE_VERSION="1.5.5"
ENV LANG ""
ENV LANGUAGE ""
ENV LC_ALL ""
# Install apptainer
RUN add-apt-repository -y ppa:apptainer/ppa \
&& apt-get update --yes \
&& DEBIAN_FRONTEND=noninteractive apt-get install --yes apptainer \
&& apt-get clean && rm -rf /var/lib/apt/lists/* \
&& rm -rf /root/.cache && rm -rf /home/${NB_USER}/.cache
# Install Apache Tomcat
RUN wget -q https://archive.apache.org/dist/tomcat/tomcat-${TOMCAT_REL}/v${TOMCAT_VERSION}/bin/apache-tomcat-${TOMCAT_VERSION}.tar.gz -P /tmp \
&& tar -xf /tmp/apache-tomcat-${TOMCAT_VERSION}.tar.gz -C /tmp \
&& rm -rf /tmp/apache-tomcat-${TOMCAT_VERSION}.tar.gz \
&& mv /tmp/apache-tomcat-${TOMCAT_VERSION} /usr/local/tomcat \
&& mv /usr/local/tomcat/webapps /usr/local/tomcat/webapps.dist \
&& mkdir /usr/local/tomcat/webapps \
&& chmod +x /usr/local/tomcat/bin/*.sh
# Install Apache Guacamole
RUN wget -q "https://archive.apache.org/dist/guacamole/${GUACAMOLE_VERSION}/binary/guacamole-${GUACAMOLE_VERSION}.war" -O /usr/local/tomcat/webapps/ROOT.war \
&& wget -q "https://archive.apache.org/dist/guacamole/${GUACAMOLE_VERSION}/source/guacamole-server-${GUACAMOLE_VERSION}.tar.gz" -P /tmp \
&& tar xvf /tmp/guacamole-server-${GUACAMOLE_VERSION}.tar.gz -C /tmp \
&& rm /tmp/guacamole-server-${GUACAMOLE_VERSION}.tar.gz \
&& cd /tmp/guacamole-server-${GUACAMOLE_VERSION} \
&& ./configure --with-init-dir=/etc/init.d \
&& make \
&& make install \
&& ldconfig \
&& rm -r /tmp/guacamole-server-${GUACAMOLE_VERSION}
# Set home directory default acls
RUN chmod g+rwxs /home/${NB_USER}
RUN setfacl -dRm u::rwX,g::rwX,o::0 /home/${NB_USER}
# #========================================#
# # Software (as root user)
# #========================================#
# Add Software sources
RUN wget -qO- https://packages.microsoft.com/keys/microsoft.asc | gpg --dearmor > packages.microsoft.gpg \
&& install -D -o root -g root -m 644 packages.microsoft.gpg /etc/apt/keyrings/packages.microsoft.gpg \
&& sh -c 'echo "deb [arch=amd64,arm64,armhf signed-by=/etc/apt/keyrings/packages.microsoft.gpg] https://packages.microsoft.com/repos/code stable main" > /etc/apt/sources.list.d/vscode.list' \
&& rm -f packages.microsoft.gpg \
&& add-apt-repository ppa:nextcloud-devs/client \
&& chmod -R 770 /home/${NB_USER}/.launchpadlib \
&& chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/.launchpadlib \
&& curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
# Workaround for CVMFS to break systemctl by replacing it with a dummy script
RUN mv /usr/bin/systemctl /usr/bin/systemctl.orig \
&& echo '#!/bin/bash' > /usr/bin/systemctl \
&& echo 'echo "systemctl is disabled in this container"' >> /usr/bin/systemctl \
&& chmod +x /usr/bin/systemctl
# Install CVMFS
RUN wget -q https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest_all.deb -P /tmp \
&& dpkg -i /tmp/cvmfs-release-latest_all.deb \
&& rm /tmp/cvmfs-release-latest_all.deb
# Install CVMFS Packages
RUN apt-get update --yes \
&& DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends cvmfs \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
# Install Tools and Libs
RUN apt-get update --yes \
&& DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends \
aria2 \
bc \
code \
davfs2 \
debootstrap \
dnsutils \
emacs \
gedit \
git \
git-annex \
gnome-keyring \
graphviz \
htop \
imagemagick \
iputils-ping \
less \
libgfortran5 \
libgpgme-dev \
libossp-uuid-dev \
libpci3 \
libreoffice \
lmod \
lua-bit32 \
lua-filesystem \
lua-json \
lua-lpeg \
lua-posix \
lua-term \
lua5.2 \
lxtask \
man-db \
nano \
nextcloud-client \
nodejs \
openssh-client \
openssh-server \
owncloud-client \
pciutils \
qdirstat \
rsync \
s3fs \
screen \
sshfs \
tcllib \
tk \
tmux \
tree \
uidmap \
unzip \
vim \
xdg-utils \
yarn \
zip \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
# Install firefox
RUN add-apt-repository ppa:mozillateam/ppa \
&& apt-get update --yes \
&& DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends \
--target-release 'o=LP-PPA-mozillateam' firefox \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
COPY config/firefox/mozillateamppa /etc/apt/preferences.d/mozillateamppa
COPY config/firefox/syspref.js /etc/firefox/syspref.js
#========================================#
# Software (as notebook user)
#========================================#
USER ${NB_USER}
# Install conda packages
RUN conda install -c conda-forge nb_conda_kernels \
&& conda clean --all -f -y \
&& rm -rf /home/${NB_USER}/.cache
RUN conda config --system --prepend envs_dirs '~/conda-environments'
# Add datalad-container datalad-osf osfclient ipyniivue to the conda environment
RUN /opt/conda/bin/pip install datalad nipype matplotlib datalad-container datalad-osf osfclient ipyniivue \
&& rm -rf /home/${NB_USER}/.cache
# Install jupyter-server-proxy and disable announcements
# Deprecated: jupyter labextension install ..
# jupyter_server_proxy needs to be at least 4.2.0 to fix CVE-2024-35225
# jupyterlmod==4.0.3 needs to be pinned for now because they broken the API after that and have not fixed it yet in 5.2.1: https://github.com/cmd-ntrf/jupyter-lmod/issues/79
RUN /opt/conda/bin/pip install jupyter-server-proxy \
&& /opt/conda/bin/jupyter labextension disable @jupyterlab/apputils-extension:announcements \
&& /opt/conda/bin/pip install jupyterlmod==4.0.3 \
&& /opt/conda/bin/pip install jupyterlab-git \
&& /opt/conda/bin/pip install jupyterlab_rise \
&& /opt/conda/bin/pip install ipycanvas \
&& /opt/conda/bin/pip install jupyter-resource-usage \
&& /opt/conda/bin/pip install jupyter_scheduler \
&& /opt/conda/bin/pip install httpx \
&& /opt/conda/bin/pip install ipywidgets ipyvolume jupyterlab_widgets \
&& rm -rf /home/${NB_USER}/.cache
#========================================#
# Configuration (as root user)
#========================================#
USER root
# Create cvmfs keys
RUN mkdir -p /etc/cvmfs/keys/ardc.edu.au
COPY config/cvmfs/neurodesk.ardc.edu.au.pub /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub
COPY config/cvmfs/neurodesk.ardc.edu.au.conf /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf
COPY config/cvmfs/neurodesk.ardc.edu.au.conf.cdn /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf.cdn
COPY config/cvmfs/neurodesk.ardc.edu.au.conf.direct /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf.direct
COPY config/cvmfs/default.local /etc/cvmfs/default.local
# # Customise logo, wallpaper, terminal
COPY config/jupyter/neurodesk_brain_logo.svg /opt/neurodesk_brain_logo.svg
COPY config/jupyter/neurodesk_brain_icon.svg /opt/neurodesk_brain_icon.svg
COPY config/lxde/background.png /usr/share/lxde/wallpapers/desktop_wallpaper.png
COPY config/lxde/pcmanfm.conf /etc/xdg/pcmanfm/LXDE/pcmanfm.conf
COPY config/lxde/lxterminal.conf /usr/share/lxterminal/lxterminal.conf
COPY config/lmod/module.sh /usr/share/
# Configure tiling of windows SHIFT-ALT-CTR-{Left,right,top,Bottom} and other openbox desktop mods
COPY ./config/lxde/rc.xml /etc/xdg/openbox
# Allow the root user to access the sshfs mount
# https://github.com/NeuroDesk/neurodesk/issues/47
RUN sed -i 's/#user_allow_other/user_allow_other/g' /etc/fuse.conf
# Fetch singularity bind mount list and create placeholder mountpoints
# RUN mkdir -p `curl https://raw.githubusercontent.com/NeuroDesk/neurocontainers/master/recipes/globalMountPointList.txt`
# Fix "No session for pid prompt"
RUN rm /usr/bin/lxpolkit
# enable rootless mounts:
RUN chmod +x /usr/bin/fusermount
# Add notebook startup scripts
# https://jupyter-docker-stacks.readthedocs.io/en/latest/using/common.html
RUN mkdir -p /usr/local/bin/start-notebook.d/ \
&& mkdir -p /usr/local/bin/before-notebook.d/
COPY config/jupyter/start_notebook.sh /usr/local/bin/start-notebook.d/
COPY config/jupyter/before_notebook.sh /usr/local/bin/before-notebook.d/
# Add jupyter notebook and startup scripts for system-wide configuration
COPY --chown=root:users config/jupyter/jupyter_notebook_config.py /etc/jupyter/jupyter_notebook_config.py
COPY --chown=root:users config/jupyter/jupyterlab_startup.sh /opt/neurodesktop/jupyterlab_startup.sh
COPY --chown=root:users config/guacamole/guacamole.sh /opt/neurodesktop/guacamole.sh
COPY --chown=root:users config/jupyter/environment_variables.sh /opt/neurodesktop/environment_variables.sh
COPY --chown=root:users config/guacamole/user-mapping.xml /etc/guacamole/user-mapping.xml
RUN chmod +x /etc/jupyter/jupyter_notebook_config.py \
/opt/neurodesktop/jupyterlab_startup.sh \
/opt/neurodesktop/guacamole.sh \
/opt/neurodesktop/environment_variables.sh
# Create Guacamole configurations (user-mapping.xml gets filled in the startup.sh script)
RUN mkdir -p /etc/guacamole \
&& echo -e "user-mapping: /etc/guacamole/user-mapping.xml\nguacd-hostname: 127.0.0.1" > /etc/guacamole/guacamole.properties \
&& echo -e "[server]\nbind_host = 127.0.0.1\nbind_port = 4822" > /etc/guacamole/guacd.conf
# Add NB_USER to sudoers
RUN echo "${NB_USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers.d/notebook \
# The following apply to Singleuser mode only. See config/jupyter/before_notebook.sh for Notebook mode
&& /usr/bin/printf '%s\n%s\n' 'password' 'password' | passwd ${NB_USER} \
&& usermod --shell /bin/bash ${NB_USER}
# Enable deletion of non-empty-directories in JupyterLab: https://github.com/jupyter/notebook/issues/4916
RUN sed -i 's/c.FileContentsManager.delete_to_trash = False/c.FileContentsManager.always_delete_dir = True/g' /etc/jupyter/jupyter_server_config.py
# Copy script to test_containers
COPY config/test_neurodesktop.sh /usr/share/test_neurodesktop.sh
# Install version 1.1.1 of fix_bash.sh that is required for test_containers
RUN chmod +x /usr/share/test_neurodesktop.sh \
&& git clone https://github.com/civier/fix_bash.git /tmp/fix_bash \
&& cd /tmp/fix_bash \
&& git checkout tags/1.1.1 \
&& cp /tmp/fix_bash/fix_bash.sh /usr/share \
&& rm -Rf /tmp/fix_bash
#========================================#
# Configuration (as notebook user)
#========================================#
# Switch to notebook user
USER ${NB_USER}
# Configure ITKsnap
RUN mkdir -p /home/${NB_USER}/.itksnap.org/ITK-SNAP \
&& chown ${NB_USER} /home/${NB_USER}/.itksnap.org -R
COPY --chown=${NB_UID}:${NB_GID} ./config/itksnap/UserPreferences.xml /home/${NB_USER}/.itksnap.org
COPY --chown=${NB_UID}:${NB_GID} ./config/lxde/mimeapps.list /home/${NB_USER}/.config/mimeapps.list
COPY --chown=${NB_UID}:${NB_GID} config/lxde/panel /home/${NB_USER}/.config/lxpanel/LXDE/panels/panel
COPY --chown=${NB_UID}:${NB_GID} config/lxde/.bashrc /home/${NB_USER}/tmp_bashrc
RUN cat /home/${NB_USER}/tmp_bashrc >> /home/${NB_USER}/.bashrc \
&& rm /home/${NB_USER}/tmp_bashrc
# Setup git
RUN git config --global user.email "[email protected]" \
&& git config --global user.name "Neurodesk User"
# Setup temp directory for matplotlib (required for fmriprep)
RUN mkdir -p /home/${NB_USER}/.config/matplotlib-mpldir \
&& chmod -R 700 /home/${NB_USER}/.config/matplotlib-mpldir \
&& chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/.config/matplotlib-mpldir
COPY --chown=${NB_UID}:${NB_GID} config/vscode/settings.json /home/${NB_USER}/.config/Code/User/settings.json
# Add libfm script
RUN mkdir -p /home/${NB_USER}/.config/libfm
COPY --chown=${NB_UID}:${NB_GID} ./config/lxde/libfm.conf /home/${NB_USER}/.config/libfm
RUN touch /home/${NB_USER}/.sudo_as_admin_successful
ENV DONT_PROMPT_WSL_INSTALL=1
ENV LMOD_CMD /usr/share/lmod/lmod/libexec/lmod
# Add startup and config files for neurodesktop, jupyter, guacamole, vnc
RUN mkdir /home/${NB_USER}/.vnc \
&& chown ${NB_USER} /home/${NB_USER}/.vnc \
&& /usr/bin/printf '%s\n%s\n%s\n' 'password' 'password' 'n' | vncpasswd
COPY --chown=${NB_UID}:${NB_GID} config/lxde/xstartup /home/${NB_USER}/.vnc
COPY --chown=${NB_UID}:${NB_GID} config/conda/conda-readme.md /home/${NB_USER}/
RUN mkdir -p /home/${NB_USER}/.ssh \
&& chmod -R 700 /home/${NB_USER}/.ssh \
&& setfacl -dRm u::rwx,g::0,o::0 /home/${NB_USER}/.ssh
COPY --chown=${NB_UID}:${NB_GID} config/ssh/sshd_config /home/${NB_USER}/.ssh/sshd_config
RUN chmod +x /home/${NB_USER}/.vnc/xstartup
# Set up working directories and symlinks
RUN mkdir -p /home/${NB_USER}/Desktop/
#========================================#
# Finalise build
#========================================#
# Switch to root user
USER root
# Save a backup copy of startup home dir into /tmp
# Used to restore home dir in persistent sessions
RUN cp -rp /home/${NB_USER} /tmp/
# Set up data directory so it exists in the container for the SINGULARITY_BINDPATH
RUN mkdir -p /data
# Install neurocommand
ADD "https://api.github.com/repos/neurodesk/neurocommand/git/refs/heads/main" /tmp/skipcache
RUN rm /tmp/skipcache \
&& git clone https://github.com/NeuroDesk/neurocommand.git /neurocommand \
&& cd /neurocommand \
&& bash build.sh --lxde --edit \
&& bash install.sh \
&& ln -s /home/${NB_USER}/neurodesktop-storage/containers /neurocommand/local/containers
USER ${NB_UID}
WORKDIR "${HOME}"
# Install example notebooks
ADD "https://api.github.com/repos/neurodesk/example-notebooks/git/refs/heads/main" /home/${NB_USER}/skipcache
RUN rm /home/${NB_USER}/skipcache \
&& git clone --depth 1 https://github.com/NeuroDesk/example-notebooks
# Set SINGULARITY_BINDPATH and MODULEPATH here so it's available within a notebook (the startup scripts set these things too late):
ENV APPTAINER_BINDPATH=/data,/mnt,/neurodesktop-storage,/tmp,/cvmfs
ENV MODULEPATH=/cvmfs/neurodesk.ardc.edu.au/containers/modules/
# This workaround is currently needed for Docker on Apple silicone - they broke normal mounting of /cvmfs in the custom docker kernel. Mounting as writable works around it.
ENV neurodesk_singularity_opts=" -w "