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ARG GO_VERSION="1.17.2"
ARG SINGULARITY_VERSION="3.9.3"
ARG TOMCAT_REL="9"
ARG TOMCAT_VERSION="9.0.58"
ARG GUACAMOLE_VERSION="1.4.0"
FROM jupyter/base-notebook:python-3.7.6
USER root
# Install base image dependancies
RUN apt-get update \
&& DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
locales \
sudo \
wget \
ca-certificates \
make \
gcc \
g++ \
openjdk-11-jre \
libpng-dev \
libjpeg-turbo8-dev \
libcairo2-dev \
libtool-bin \
libossp-uuid-dev \
libwebp-dev \
lxde \
openssh-server \
libpango1.0-dev \
libssh2-1-dev \
libssl-dev \
openssh-server \
libvncserver-dev \
libxt6 \
xauth \
xorg \
freerdp2-dev \
xrdp \
xauth \
xorg \
xorgxrdp \
tigervnc-standalone-server \
tigervnc-common \
lxterminal \
lxrandr \
curl \
gpg \
software-properties-common \
dbus-x11 \
&& rm -rf /var/lib/apt/lists/*
# Set locale
RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
&& locale-gen
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8
# Install Apache Guacamole
ARG GUACAMOLE_VERSION
WORKDIR /etc/guacamole
RUN wget "https://apache.mirror.digitalpacific.com.au/guacamole/${GUACAMOLE_VERSION}/source/guacamole-server-${GUACAMOLE_VERSION}.tar.gz" -O /etc/guacamole/guacamole-server-${GUACAMOLE_VERSION}.tar.gz \
&& tar xvf /etc/guacamole/guacamole-server-${GUACAMOLE_VERSION}.tar.gz \
&& cd /etc/guacamole/guacamole-server-${GUACAMOLE_VERSION} \
&& ./configure --with-init-dir=/etc/init.d \
&& make \
&& make install \
&& ldconfig \
&& rm -r /etc/guacamole/guacamole-server-${GUACAMOLE_VERSION}*
# Create Guacamole configurations
COPY --chown=root:root config/user-mapping.xml /etc/guacamole/user-mapping.xml
COPY --chown=root:root config/guacamole.properties /etc/guacamole/guacamole.properties
COPY --chown=root:root config/guacd.conf /etc/guacamole/guacd.conf
# Add Visual Studio code and nextcloud client
RUN curl https://packages.microsoft.com/keys/microsoft.asc | gpg --dearmor > microsoft.gpg \
&& mv microsoft.gpg /etc/apt/trusted.gpg.d/microsoft.gpg \
&& echo "deb [arch=amd64] http://packages.microsoft.com/repos/vscode stable main" | tee /etc/apt/sources.list.d/vs-code.list \
&& add-apt-repository ppa:nextcloud-devs/client
# Add CVMFS
RUN wget https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest_all.deb \
&& dpkg -i cvmfs-release-latest_all.deb \
&& rm cvmfs-release-latest_all.deb
# Install basic tools
RUN apt-get update \
&& DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
cryptsetup \
squashfs-tools \
lua-bit32 \
lua-filesystem \
lua-json \
lua-lpeg \
lua-posix \
lua-term \
lua5.2 \
lmod \
git \
aria2 \
code \
emacs \
gedit \
htop \
imagemagick \
less \
nano \
openssh-client \
python3-pip \
rsync \
screen \
tree \
vim \
gcc \
python3-dev \
graphviz \
libzstd1 \
libgfortran5 \
zlib1g-dev \
zip \
unzip \
nextcloud-client \
iputils-ping \
sshfs \
build-essential \
uuid-dev \
libgpgme-dev \
squashfs-tools \
libseccomp-dev \
wget \
pkg-config \
cryptsetup-bin\
lsb-release \
cvmfs \
rclone \
davfs2 \
owncloud-client \
firefox \
&& rm -rf /var/lib/apt/lists/* \
&& rm /etc/apt/sources.list.d/vs-code.list
# Configure CVMFS
RUN mkdir -p /etc/cvmfs/keys/ardc.edu.au/ \
&& echo "-----BEGIN PUBLIC KEY-----" | sudo tee /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub \
&& echo "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAwUPEmxDp217SAtZxaBep" | sudo tee -a /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub \
&& echo "Bi2TQcLoh5AJ//HSIz68ypjOGFjwExGlHb95Frhu1SpcH5OASbV+jJ60oEBLi3sD" | sudo tee -a /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub \
&& echo "qA6rGYt9kVi90lWvEjQnhBkPb0uWcp1gNqQAUocybCzHvoiG3fUzAe259CrK09qR" | sudo tee -a /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub \
&& echo "pX8sZhgK3eHlfx4ycyMiIQeg66AHlgVCJ2fKa6fl1vnh6adJEPULmn6vZnevvUke" | sudo tee -a /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub \
&& echo "I6U1VcYTKm5dPMrOlY/fGimKlyWvivzVv1laa5TAR2Dt4CfdQncOz+rkXmWjLjkD" | sudo tee -a /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub \
&& echo "87WMiTgtKybsmMLb2yCGSgLSArlSWhbMA0MaZSzAwE9PJKCCMvTANo5644zc8jBe" | sudo tee -a /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub \
&& echo "NQIDAQAB" | sudo tee -a /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub \
&& echo "-----END PUBLIC KEY-----" | sudo tee -a /etc/cvmfs/keys/ardc.edu.au/neurodesk.ardc.edu.au.pub \
&& echo "CVMFS_USE_GEOAPI=yes" | sudo tee /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf \
&& echo 'CVMFS_SERVER_URL="http://203.101.231.144/cvmfs/@fqrn@;http://150.136.239.221/cvmfs/@fqrn@;http://132.145.96.34/cvmfs/@fqrn@;http://140.238.170.185/cvmfs/@fqrn@;http://130.61.74.69/cvmfs/@fqrn@;http://152.67.114.42/cvmfs/@fqrn@"' | sudo tee -a /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf \
&& echo 'CVMFS_KEYS_DIR="/etc/cvmfs/keys/ardc.edu.au/"' | sudo tee -a /etc/cvmfs/config.d/neurodesk.ardc.edu.au.conf \
&& echo "CVMFS_HTTP_PROXY=DIRECT" | sudo tee /etc/cvmfs/default.local \
&& echo "CVMFS_QUOTA_LIMIT=5000" | sudo tee -a /etc/cvmfs/default.local \
&& cvmfs_config setup
# Add module script
COPY ./config/module.sh /usr/share/
# Install nipype
RUN pip3 install nipype \
&& rm -rf /root/.cache/pip \
&& rm -rf /home/ubuntu/.cache/
# Configure tiling of windows SHIFT-ALT-CTR-{Left,right,top,Bottom} and other openbox desktop mods
COPY ./config/rc.xml /etc/xdg/openbox
# Configure ITKsnap
COPY ./config/.itksnap.org /home/jovyan/.itksnap.org
RUN chown jovyan /home/jovyan/.itksnap.org -R
COPY ./config/mimeapps.list /home/jovyan/.config/mimeapps.list
# Apply custom bottom panel configuration
COPY ./config/panel /home/jovyan/.config/lxpanel/LXDE/panels/panel
# 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
RUN mkdir -p `curl https://raw.githubusercontent.com/NeuroDesk/neurocontainers/master/recipes/globalMountPointList.txt`
# Fix "No session for pid prompt"
RUN mv /usr/bin/lxpolkit /usr/bin/lxpolkit.BAK
USER jovyan
WORKDIR /home/jovyan
# Create user account with password-less sudo abilities and vnc user
RUN mkdir /home/jovyan/.vnc \
&& chown jovyan /home/jovyan/.vnc \
&& /usr/bin/printf '%s\n%s\n%s\n' 'password' 'password' 'n' | vncpasswd
# Install Apache Tomcat
ARG TOMCAT_REL
ARG TOMCAT_VERSION
RUN wget 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 \
&& mv /tmp/apache-tomcat-${TOMCAT_VERSION} /home/jovyan/.tomcat \
&& rm -rf /home/jovyan/.tomcat/webapps/* \
&& wget "https://apache.mirror.digitalpacific.com.au/guacamole/${GUACAMOLE_VERSION}/binary/guacamole-${GUACAMOLE_VERSION}.war" -O /home/jovyan/.tomcat/webapps/ROOT.war
RUN pip install jupyter-server-proxy
COPY config/jupyter_notebook_config.py /home/jovyan/.jupyter
COPY --chown=jovyan:users config/neurodesktop.sh /home/jovyan/.neurodesktop.sh
RUN chmod +x /home/jovyan/.neurodesktop.sh
USER root
# Install singularity
ARG GO_VERSION
ARG SINGULARITY_VERSION
RUN export VERSION=${GO_VERSION} OS=linux ARCH=amd64 \
&& wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz \
&& sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz \
&& rm go$VERSION.$OS-$ARCH.tar.gz \
&& export GOPATH=${HOME}/go \
&& export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin \
&& mkdir -p $GOPATH/src/github.com/sylabs \
&& cd $GOPATH/src/github.com/sylabs \
&& wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz \
&& tar -xzvf singularity-ce-${SINGULARITY_VERSION}.tar.gz \
&& cd singularity-ce-${SINGULARITY_VERSION} \
&& ./mconfig --without-suid -p /usr/local/singularity \
&& make -C builddir \
&& make -C builddir install \
&& rm -rf /usr/local/go $GOPATH
# add Globus client
WORKDIR /opt/globusconnectpersonal
RUN apt-get update \
&& DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
tk \
tcllib \
&& rm -rf /var/lib/apt/lists/* \
&& wget https://downloads.globus.org/globus-connect-personal/linux/stable/globusconnectpersonal-latest.tgz \
&& tar xzf globusconnectpersonal-latest.tgz \
&& rm -rf globusconnectpersonal-latest.tgz
# Desktop styling
COPY config/desktop_wallpaper.jpg /usr/share/lxde/wallpapers/desktop_wallpaper.jpg
COPY config/pcmanfm.conf /etc/xdg/pcmanfm/LXDE/pcmanfm.conf
COPY config/lxterminal.conf /usr/share/lxterminal/lxterminal.conf
# Change firefox home
RUN echo 'pref("browser.startup.homepage", "http://neurodesk.github.io", locked);' >> /etc/firefox/syspref.js \
&& echo 'pref("browser.startup.firstrunSkipsHomepage", true, locked);' >> /etc/firefox/syspref.js \
&& echo 'pref("startup.homepage_welcome_url", "http://neurodesk.github.io", locked);' >> /etc/firefox/syspref.js \
&& echo 'pref("browser.aboutwelcome.enabled", true, locked);' >> /etc/firefox/syspref.js
# Create link to persistent storage on Desktop (This needs to happen before the users gets created!)
RUN mkdir /neurodesktop-storage && chown -R jovyan:users /neurodesktop-storage
RUN mkdir -p /home/jovyan/Desktop/ \
&& ln -s /neurodesktop-storage /home/jovyan/Desktop/
# Install neurodesk
ADD "http://api.github.com/repos/NeuroDesk/neurocommand/commits/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 /neurodesktop-storage/containers /neurocommand/local/containers
COPY config/neurodesk.ardc.edu.au.conf /cvmfs/neurodesk.ardc.edu.au.conf
RUN mkdir -p /cvmfs/neurodesk.ardc.edu.au /cvmfs/cache/neurodesk.ardc.edu.au /cvmfs/logs/
RUN chown -R jovyan:users /cvmfs/neurodesk.ardc.edu.au /cvmfs/logs /cvmfs/cache
# RUN wget https://developer.download.nvidia.com/compute/cuda/11.5.0/local_installers/cuda_11.5.0_495.29.05_linux.run \
# && chmod +x cuda_11.5.0_495.29.05_linux.run \
# && ./cuda_11.5.0_495.29.05_linux.run --toolkit --silent --override \
# && rm cuda_11.5.0_495.29.05_linux.run
USER jovyan
WORKDIR /home/jovyan
# Setup module system & singularity
COPY ./config/.bashrc /home/jovyan/tmp_bashrc
RUN cat /home/jovyan/tmp_bashrc >> /home/jovyan/.bashrc && rm /home/jovyan/tmp_bashrc \
&& directories=`curl https://raw.githubusercontent.com/NeuroDesk/caid/master/recipes/globalMountPointList.txt` \
&& mounts=`echo $directories | sed 's/ /,/g'` \
&& echo "export SINGULARITY_BINDPATH=${mounts},/neurodesktop-storage" >> /home/jovyan/.bashrc
# Link vscode config to persistant storage
RUN mkdir -p /home/jovyan/.config \
&& ln -s /neurodesktop-storage/.config/Code .config/Code \
&& ln -s /neurodesktop-storage/.vscode .vscode