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FROM ubuntu:20.04
USER root
### BASICS ###
# Technical Environment Variables
ENV \
SHELL="/bin/bash" \
HOME="/root" \
# Nobteook server user: https://github.com/jupyter/docker-stacks/blob/master/base-notebook/Dockerfile#L33
NB_USER="root" \
USER_GID=0 \
XDG_CACHE_HOME="/root/.cache/" \
XDG_RUNTIME_DIR="/tmp" \
DISPLAY=":1" \
TERM="xterm" \
DEBIAN_FRONTEND="noninteractive" \
RESOURCES_PATH="/resources" \
SSL_RESOURCES_PATH="/resources/ssl" \
WORKSPACE_HOME="/workspace"
WORKDIR $HOME
# Make folders
RUN \
mkdir $RESOURCES_PATH && chmod a+rwx $RESOURCES_PATH && \
mkdir $WORKSPACE_HOME && chmod a+rwx $WORKSPACE_HOME && \
mkdir $SSL_RESOURCES_PATH && chmod a+rwx $SSL_RESOURCES_PATH
# Layer cleanup script
COPY resources/scripts/clean-layer.sh /usr/bin/clean-layer.sh
COPY resources/scripts/fix-permissions.sh /usr/bin/fix-permissions.sh
# Make clean-layer and fix-permissions executable
RUN \
chmod a+rwx /usr/bin/clean-layer.sh && \
chmod a+rwx /usr/bin/fix-permissions.sh
# Generate and Set locals
# https://stackoverflow.com/questions/28405902/how-to-set-the-locale-inside-a-debian-ubuntu-docker-container#38553499
RUN \
apt-get update && \
apt-get install -y locales && \
# install locales-all?
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
locale-gen && \
dpkg-reconfigure --frontend=noninteractive locales && \
update-locale LANG=en_US.UTF-8 && \
# Cleanup
clean-layer.sh
ENV LC_ALL="en_US.UTF-8" \
LANG="en_US.UTF-8" \
LANGUAGE="en_US:en"
# Install basics
RUN \
# TODO add repos?
# add-apt-repository ppa:apt-fast/stable
# add-apt-repository 'deb http://security.ubuntu.com/ubuntu xenial-security main'
apt-get update --fix-missing && \
apt-get install -y sudo apt-utils && \
apt-get upgrade -y && \
apt-get update && \
apt-get install -y --no-install-recommends \
# This is necessary for apt to access HTTPS sources:
apt-transport-https \
gnupg-agent \
gpg-agent \
gnupg2 \
ca-certificates \
build-essential \
pkg-config \
software-properties-common \
lsof \
net-tools \
libcurl4 \
curl \
wget \
cron \
openssl \
iproute2 \
psmisc \
tmux \
dpkg-sig \
uuid-dev \
csh \
xclip \
clinfo \
time \
libssl-dev \
libgdbm-dev \
libncurses5-dev \
libncursesw5-dev \
# required by pyenv
libreadline-dev \
libedit-dev \
xz-utils \
gawk \
# Simplified Wrapper and Interface Generator (5.8MB) - required by lots of py-libs
swig \
# Graphviz (graph visualization software) (4MB)
graphviz libgraphviz-dev \
# Terminal multiplexer
screen \
# Editor
nano \
# Find files
locate \
# Dev Tools
sqlite3 \
# XML Utils
xmlstarlet \
# GNU parallel
parallel \
# R*-tree implementation - Required for earthpy, geoviews (3MB)
libspatialindex-dev \
# Search text and binary files
yara \
# Minimalistic C client for Redis
libhiredis-dev \
# postgresql client
libpq-dev \
# mysql client (10MB)
libmysqlclient-dev \
# mariadb client (7MB)
# libmariadbclient-dev \
# image processing library (6MB), required for tesseract
libleptonica-dev \
# GEOS library (3MB)
libgeos-dev \
# style sheet preprocessor
less \
# Print dir tree
tree \
# Bash autocompletion functionality
bash-completion \
# ping support
iputils-ping \
# Map remote ports to localhosM
socat \
# Json Processor
jq \
rsync \
# sqlite3 driver - required for pyenv
libsqlite3-dev \
# VCS:
git \
subversion \
jed \
# odbc drivers
unixodbc unixodbc-dev \
# Image support
libtiff-dev \
libjpeg-dev \
libpng-dev \
libglib2.0-0 \
libxext6 \
libsm6 \
libxext-dev \
libxrender1 \
libzmq3-dev \
# protobuffer support
protobuf-compiler \
libprotobuf-dev \
libprotoc-dev \
autoconf \
automake \
libtool \
cmake \
fonts-liberation \
google-perftools \
# Compression Libs
# also install rar/unrar? but both are propriatory or unar (40MB)
zip \
gzip \
unzip \
bzip2 \
lzop \
# deprecates bsdtar (https://ubuntu.pkgs.org/20.04/ubuntu-universe-i386/libarchive-tools_3.4.0-2ubuntu1_i386.deb.html)
libarchive-tools \
zlibc \
# unpack (almost) everything with one command
unp \
libbz2-dev \
liblzma-dev \
zlib1g-dev && \
# Update git to newest version
add-apt-repository -y ppa:git-core/ppa && \
apt-get update && \
apt-get install -y --no-install-recommends git && \
# Fix all execution permissions
chmod -R a+rwx /usr/local/bin/ && \
# configure dynamic linker run-time bindings
ldconfig && \
# Fix permissions
fix-permissions.sh $HOME && \
# Cleanup
clean-layer.sh
# Add tini
RUN wget --no-verbose https://github.com/krallin/tini/releases/download/v0.19.0/tini -O /tini && \
chmod +x /tini
# prepare ssh for inter-container communication for remote python kernel
RUN \
apt-get update && \
apt-get install -y --no-install-recommends \
openssh-client \
openssh-server \
# SSLH for SSH + HTTP(s) Multiplexing
sslh \
# SSH Tooling
autossh \
mussh && \
chmod go-w $HOME && \
mkdir -p $HOME/.ssh/ && \
# create empty config file if not exists
touch $HOME/.ssh/config && \
sudo chown -R $NB_USER:users $HOME/.ssh && \
chmod 700 $HOME/.ssh && \
printenv >> $HOME/.ssh/environment && \
chmod -R a+rwx /usr/local/bin/ && \
# Fix permissions
fix-permissions.sh $HOME && \
# Cleanup
clean-layer.sh
RUN \
OPEN_RESTY_VERSION="1.19.3.2" && \
mkdir $RESOURCES_PATH"/openresty" && \
cd $RESOURCES_PATH"/openresty" && \
apt-get update && \
apt-get purge -y nginx nginx-common && \
# libpcre required, otherwise you get a 'the HTTP rewrite module requires the PCRE library' error
# Install apache2-utils to generate user:password file for nginx.
apt-get install -y libssl-dev libpcre3 libpcre3-dev apache2-utils && \
wget --no-verbose https://openresty.org/download/openresty-$OPEN_RESTY_VERSION.tar.gz -O ./openresty.tar.gz && \
tar xfz ./openresty.tar.gz && \
rm ./openresty.tar.gz && \
cd ./openresty-$OPEN_RESTY_VERSION/ && \
# Surpress output - if there is a problem remove > /dev/null
./configure --with-http_stub_status_module --with-http_sub_module > /dev/null && \
make -j2 > /dev/null && \
make install > /dev/null && \
# create log dir and file - otherwise openresty will throw an error
mkdir -p /var/log/nginx/ && \
touch /var/log/nginx/upstream.log && \
cd $RESOURCES_PATH && \
rm -r $RESOURCES_PATH"/openresty" && \
# Fix permissions
chmod -R a+rwx $RESOURCES_PATH && \
# Cleanup
clean-layer.sh
ENV PATH=/usr/local/openresty/nginx/sbin:$PATH
COPY resources/nginx/lua-extensions /etc/nginx/nginx_plugins
### END BASICS ###
### RUNTIMES ###
# Install Miniconda: https://repo.continuum.io/miniconda/
ENV \
# TODO: CONDA_DIR is deprecated and should be removed in the future
CONDA_DIR=/opt/conda \
CONDA_ROOT=/opt/conda \
PYTHON_VERSION="3.8.10" \
CONDA_PYTHON_DIR=/opt/conda/lib/python3.8 \
MINICONDA_VERSION=4.9.2 \
MINICONDA_MD5=122c8c9beb51e124ab32a0fa6426c656 \
CONDA_VERSION=4.9.2
RUN wget --no-verbose https://repo.anaconda.com/miniconda/Miniconda3-py38_${CONDA_VERSION}-Linux-x86_64.sh -O ~/miniconda.sh && \
echo "${MINICONDA_MD5} *miniconda.sh" | md5sum -c - && \
/bin/bash ~/miniconda.sh -b -p $CONDA_ROOT && \
export PATH=$CONDA_ROOT/bin:$PATH && \
rm ~/miniconda.sh && \
# Configure conda
# TODO: Add conde-forge as main channel -> remove if testted
# TODO, use condarc file
$CONDA_ROOT/bin/conda config --system --add channels conda-forge && \
$CONDA_ROOT/bin/conda config --system --set auto_update_conda False && \
$CONDA_ROOT/bin/conda config --system --set show_channel_urls True && \
$CONDA_ROOT/bin/conda config --system --set channel_priority strict && \
# Deactivate pip interoperability (currently default), otherwise conda tries to uninstall pip packages
$CONDA_ROOT/bin/conda config --system --set pip_interop_enabled false && \
# Update conda
$CONDA_ROOT/bin/conda update -y -n base -c defaults conda && \
$CONDA_ROOT/bin/conda update -y setuptools && \
$CONDA_ROOT/bin/conda install -y conda-build && \
# Update selected packages - install python 3.8.x
$CONDA_ROOT/bin/conda install -y --update-all python=$PYTHON_VERSION && \
# Link Conda
ln -s $CONDA_ROOT/bin/python /usr/local/bin/python && \
ln -s $CONDA_ROOT/bin/conda /usr/bin/conda && \
# Update
$CONDA_ROOT/bin/conda install -y pip && \
$CONDA_ROOT/bin/pip install --upgrade pip && \
chmod -R a+rwx /usr/local/bin/ && \
# Cleanup - Remove all here since conda is not in path as of now
# find /opt/conda/ -follow -type f -name '*.a' -delete && \
# find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
$CONDA_ROOT/bin/conda clean -y --packages && \
$CONDA_ROOT/bin/conda clean -y -a -f && \
$CONDA_ROOT/bin/conda build purge-all && \
# Fix permissions
fix-permissions.sh $CONDA_ROOT && \
clean-layer.sh
ENV PATH=$CONDA_ROOT/bin:$PATH
# There is nothing added yet to LD_LIBRARY_PATH, so we can overwrite
ENV LD_LIBRARY_PATH=$CONDA_ROOT/lib
# Install pyenv to allow dynamic creation of python versions
RUN git clone https://github.com/pyenv/pyenv.git $RESOURCES_PATH/.pyenv && \
# Install pyenv plugins based on pyenv installer
git clone https://github.com/pyenv/pyenv-virtualenv.git $RESOURCES_PATH/.pyenv/plugins/pyenv-virtualenv && \
git clone git://github.com/pyenv/pyenv-doctor.git $RESOURCES_PATH/.pyenv/plugins/pyenv-doctor && \
git clone https://github.com/pyenv/pyenv-update.git $RESOURCES_PATH/.pyenv/plugins/pyenv-update && \
git clone https://github.com/pyenv/pyenv-which-ext.git $RESOURCES_PATH/.pyenv/plugins/pyenv-which-ext && \
apt-get update && \
# TODO: lib might contain high vulnerability
# Required by pyenv
apt-get install -y --no-install-recommends libffi-dev && \
clean-layer.sh
# Add pyenv to path
ENV PATH=$RESOURCES_PATH/.pyenv/shims:$RESOURCES_PATH/.pyenv/bin:$PATH \
PYENV_ROOT=$RESOURCES_PATH/.pyenv
# Install pipx
RUN pip install pipx && \
# Configure pipx
python -m pipx ensurepath && \
# Cleanup
clean-layer.sh
ENV PATH=$HOME/.local/bin:$PATH
# Install node.js
RUN \
apt-get update && \
# https://nodejs.org/en/about/releases/ use even numbered releases, i.e. LTS versions
curl -sL https://deb.nodesource.com/setup_14.x | sudo -E bash - && \
apt-get install -y nodejs && \
# As conda is first in path, the commands 'node' and 'npm' reference to the version of conda.
# Replace those versions with the newly installed versions of node
rm -f /opt/conda/bin/node && ln -s /usr/bin/node /opt/conda/bin/node && \
rm -f /opt/conda/bin/npm && ln -s /usr/bin/npm /opt/conda/bin/npm && \
# Fix permissions
chmod a+rwx /usr/bin/node && \
chmod a+rwx /usr/bin/npm && \
# Fix node versions - put into own dir and before conda:
mkdir -p /opt/node/bin && \
ln -s /usr/bin/node /opt/node/bin/node && \
ln -s /usr/bin/npm /opt/node/bin/npm && \
# Update npm
/usr/bin/npm install -g npm && \
# Install Yarn
/usr/bin/npm install -g yarn && \
# Install typescript
/usr/bin/npm install -g typescript && \
# Install webpack - 32 MB
/usr/bin/npm install -g webpack && \
# Install node-gyp
/usr/bin/npm install -g node-gyp && \
# Update all packages to latest version
/usr/bin/npm update -g && \
# Cleanup
clean-layer.sh
ENV PATH=/opt/node/bin:$PATH
# Java - removed
### END RUNTIMES ###
### PROCESS TOOLS ###
# Removed XRDP
# Install supervisor for process supervision
RUN \
apt-get update && \
# Create sshd run directory - required for starting process via supervisor
mkdir -p /var/run/sshd && chmod 400 /var/run/sshd && \
# Install rsyslog for syslog logging
apt-get install -y --no-install-recommends rsyslog && \
pipx install supervisor && \
pipx inject supervisor supervisor-stdout && \
# supervisor needs this logging path
mkdir -p /var/log/supervisor/ && \
# Cleanup
clean-layer.sh
### END PROCESS TOOLS ###
### GUI TOOLS ###
# Install xfce4 & gui tools
RUN \
# Use staging channel to get newest xfce4 version (4.16)
add-apt-repository -y ppa:xubuntu-dev/staging && \
apt-get update && \
apt-get install -y --no-install-recommends xfce4 && \
apt-get install -y --no-install-recommends gconf2 && \
apt-get install -y --no-install-recommends xfce4-terminal && \
apt-get install -y --no-install-recommends xfce4-clipman && \
apt-get install -y --no-install-recommends xterm && \
apt-get install -y --no-install-recommends --allow-unauthenticated xfce4-taskmanager && \
# Install dependencies to enable vncserver
apt-get install -y --no-install-recommends xauth xinit dbus-x11 && \
# Install gdebi deb installer
apt-get install -y --no-install-recommends gdebi && \
# Search for files
apt-get install -y --no-install-recommends catfish && \
apt-get install -y --no-install-recommends font-manager && \
# vs support for thunar
apt-get install -y thunar-vcs-plugin && \
# Streaming text editor for large files - klogg is alternative to glogg
apt-get install -y --no-install-recommends libqt5concurrent5 libqt5widgets5 libqt5xml5 && \
wget --no-verbose https://github.com/variar/klogg/releases/download/v20.12/klogg-20.12.0.813-Linux.deb -O $RESOURCES_PATH/klogg.deb && \
dpkg -i $RESOURCES_PATH/klogg.deb && \
rm $RESOURCES_PATH/klogg.deb && \
# Disk Usage Visualizer
apt-get install -y --no-install-recommends baobab && \
# Lightweight text editor
apt-get install -y --no-install-recommends mousepad && \
apt-get install -y --no-install-recommends vim && \
# Process monitoring
apt-get install -y --no-install-recommends htop && \
# Install Archive/Compression Tools: https://wiki.ubuntuusers.de/Archivmanager/
apt-get install -y p7zip p7zip-rar && \
apt-get install -y --no-install-recommends thunar-archive-plugin && \
apt-get install -y xarchiver && \
# DB Utils
apt-get install -y --no-install-recommends sqlitebrowser && \
# Install nautilus and support for sftp mounting
apt-get install -y --no-install-recommends nautilus gvfs-backends && \
# Install gigolo - Access remote systems
apt-get install -y --no-install-recommends gigolo gvfs-bin && \
# xfce systemload panel plugin - needs to be activated
# apt-get install -y --no-install-recommends xfce4-systemload-plugin && \
# Leightweight ftp client that supports sftp, http, ...
apt-get install -y --no-install-recommends gftp && \
# Install chrome
# sudo add-apt-repository ppa:system76/pop
add-apt-repository ppa:saiarcot895/chromium-beta && \
apt-get update && \
apt-get install -y chromium-browser chromium-browser-l10n chromium-codecs-ffmpeg && \
ln -s /usr/bin/chromium-browser /usr/bin/google-chrome && \
# Cleanup
apt-get purge -y pm-utils xscreensaver* && \
# Large package: gnome-user-guide 50MB app-install-data 50MB
apt-get remove -y app-install-data gnome-user-guide && \
clean-layer.sh
# Add the defaults from /lib/x86_64-linux-gnu, otherwise lots of no version errors
# cannot be added above otherwise there are errors in the installation of the gui tools
# Call order: https://unix.stackexchange.com/questions/367600/what-is-the-order-that-linuxs-dynamic-linker-searches-paths-in
ENV LD_LIBRARY_PATH=/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:$CONDA_ROOT/lib
# Install VNC
RUN \
apt-get update && \
# required for websockify
# apt-get install -y python-numpy && \
cd ${RESOURCES_PATH} && \
# Tiger VNC
wget -qO- https://sourceforge.net/projects/tigervnc/files/stable/1.11.0/tigervnc-1.11.0.x86_64.tar.gz/download | tar xz --strip 1 -C / && \
# Install websockify
mkdir -p ./novnc/utils/websockify && \
# Before updating the noVNC version, we need to make sure that our monkey patching scripts still work!!
wget -qO- https://github.com/novnc/noVNC/archive/v1.2.0.tar.gz | tar xz --strip 1 -C ./novnc && \
wget -qO- https://github.com/novnc/websockify/archive/v0.9.0.tar.gz | tar xz --strip 1 -C ./novnc/utils/websockify && \
chmod +x -v ./novnc/utils/*.sh && \
# create user vnc directory
mkdir -p $HOME/.vnc && \
# Fix permissions
fix-permissions.sh ${RESOURCES_PATH} && \
# Cleanup
clean-layer.sh
# Install Web Tools - Offered via Jupyter Tooling Plugin
## VS Code Server: https://github.com/codercom/code-server
COPY resources/tools/vs-code-server.sh $RESOURCES_PATH/tools/vs-code-server.sh
RUN \
/bin/bash $RESOURCES_PATH/tools/vs-code-server.sh --install && \
# Cleanup
clean-layer.sh
## ungit
COPY resources/tools/ungit.sh $RESOURCES_PATH/tools/ungit.sh
RUN \
/bin/bash $RESOURCES_PATH/tools/ungit.sh --install && \
# Cleanup
clean-layer.sh
## netdata
COPY resources/tools/netdata.sh $RESOURCES_PATH/tools/netdata.sh
RUN \
/bin/bash $RESOURCES_PATH/tools/netdata.sh --install && \
# Cleanup
clean-layer.sh
## Glances webtool is installed in python section below via requirements.txt
## Filebrowser
COPY resources/tools/filebrowser.sh $RESOURCES_PATH/tools/filebrowser.sh
RUN \
/bin/bash $RESOURCES_PATH/tools/filebrowser.sh --install && \
# Cleanup
clean-layer.sh
ARG ARG_WORKSPACE_FLAVOR="full"
ENV WORKSPACE_FLAVOR=$ARG_WORKSPACE_FLAVOR
# Install Visual Studio Code
COPY resources/tools/vs-code-desktop.sh $RESOURCES_PATH/tools/vs-code-desktop.sh
RUN \
# If minimal flavor - do not install
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
exit 0 ; \
fi && \
/bin/bash $RESOURCES_PATH/tools/vs-code-desktop.sh --install && \
# Cleanup
clean-layer.sh
# Install Firefox
COPY resources/tools/firefox.sh $RESOURCES_PATH/tools/firefox.sh
RUN \
# If minimal flavor - do not install
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
exit 0 ; \
fi && \
/bin/bash $RESOURCES_PATH/tools/firefox.sh --install && \
# Cleanup
clean-layer.sh
### END GUI TOOLS ###
### DATA SCIENCE BASICS ###
## Python 3
# Data science libraries requirements
COPY resources/libraries ${RESOURCES_PATH}/libraries
### Install main data science libs
RUN \
# Link Conda - All python are linke to the conda instances
# Linking python 3 crashes conda -> cannot install anyting - remove instead
# ln -s -f $CONDA_ROOT/bin/python /usr/bin/python3 && \
# if removed -> cannot use add-apt-repository
# rm /usr/bin/python3 && \
# rm /usr/bin/python3.5
ln -s -f $CONDA_ROOT/bin/python /usr/bin/python && \
apt-get update && \
# upgrade pip
pip install --upgrade pip && \
# If minimal flavor - install
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
# Install nomkl - mkl needs lots of space
conda install -y --update-all 'python='$PYTHON_VERSION nomkl ; \
else \
# Install mkl for faster computations
conda install -y --update-all 'python='$PYTHON_VERSION mkl-service mkl ; \
fi && \
# Install some basics - required to run container
conda install -y --update-all \
'python='$PYTHON_VERSION \
'ipython=7.24.*' \
'notebook=6.4.*' \
'jupyterlab=3.0.*' \
# TODO: nbconvert 6.x makes problems with template_path
'nbconvert=5.6.*' \
# TODO: temp fix: yarl version 1.5 is required for lots of libraries.
'yarl==1.5.*' \
# TODO install scipy, numpy, sklearn, and numexpr via conda for mkl optimizaed versions: https://docs.anaconda.com/mkl-optimizations/
'scipy==1.7.*' \
'numpy==1.19.*' \
scikit-learn \
numexpr && \
# installed via apt-get and pip: protobuf \
# installed via apt-get: zlib && \
# Switch of channel priority, makes some trouble
conda config --system --set channel_priority false && \
# Install minimal pip requirements
pip install --no-cache-dir --upgrade --upgrade-strategy only-if-needed -r ${RESOURCES_PATH}/libraries/requirements-minimal.txt && \
# If minimal flavor - exit here
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
# Remove pandoc - package for markdown conversion - not needed
# TODO: conda remove -y --force pandoc && \
# Fix permissions
fix-permissions.sh $CONDA_ROOT && \
# Cleanup
clean-layer.sh && \
exit 0 ; \
fi && \
# OpenMPI support
apt-get install -y --no-install-recommends libopenmpi-dev openmpi-bin && \
conda install -y --freeze-installed \
'python='$PYTHON_VERSION \
boost \
mkl-include && \
# Install mkldnn
conda install -y --freeze-installed -c mingfeima mkldnn && \
# Install pytorch - cpu only
conda install -y -c pytorch "pytorch==1.9.*" cpuonly && \
# Install light pip requirements
pip install --no-cache-dir --upgrade --upgrade-strategy only-if-needed -r ${RESOURCES_PATH}/libraries/requirements-light.txt && \
# If light light flavor - exit here
if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
# Fix permissions
fix-permissions.sh $CONDA_ROOT && \
# Cleanup
clean-layer.sh && \
exit 0 ; \
fi && \
# libartals == 40MB liblapack-dev == 20 MB
apt-get install -y --no-install-recommends liblapack-dev libatlas-base-dev libeigen3-dev libblas-dev && \
# pandoc -> installs libluajit -> problem for openresty
# HDF5 (19MB)
apt-get install -y --no-install-recommends libhdf5-dev && \
# TBB threading optimization
apt-get install -y --no-install-recommends libtbb-dev && \
# required for tesseract: 11MB - tesseract-ocr-dev?
apt-get install -y --no-install-recommends libtesseract-dev && \
pip install --no-cache-dir tesserocr && \
# TODO: installs tenserflow 2.4 - Required for tensorflow graphics (9MB)
apt-get install -y --no-install-recommends libopenexr-dev && \
#pip install --no-cache-dir tensorflow-graphics==2020.5.20 && \
# GCC OpenMP (GOMP) support library
apt-get install -y --no-install-recommends libgomp1 && \
# Install Intel(R) Compiler Runtime - numba optimization
# TODO: don't install, results in memory error: conda install -y --freeze-installed -c numba icc_rt && \
# Install libjpeg turbo for speedup in image processing
conda install -y --freeze-installed libjpeg-turbo && \
# Add snakemake for workflow management
conda install -y -c bioconda -c conda-forge snakemake-minimal && \
# Add mamba as conda alternativ
conda install -y -c conda-forge mamba && \
# Faiss - A library for efficient similarity search and clustering of dense vectors.
conda install -y --freeze-installed faiss-cpu && \
# Install full pip requirements
pip install --no-cache-dir --upgrade --upgrade-strategy only-if-needed --use-deprecated=legacy-resolver -r ${RESOURCES_PATH}/libraries/requirements-full.txt && \
# Setup Spacy
# Spacy - download and large language removal
python -m spacy download en && \
# Fix permissions
fix-permissions.sh $CONDA_ROOT && \
# Cleanup
clean-layer.sh
# Fix conda version
RUN \
# Conda installs wrong node version - relink conda node to the actual node
rm -f /opt/conda/bin/node && ln -s /usr/bin/node /opt/conda/bin/node && \
rm -f /opt/conda/bin/npm && ln -s /usr/bin/npm /opt/conda/bin/npm
### END DATA SCIENCE BASICS ###
### JUPYTER ###
COPY \
resources/jupyter/start.sh \
resources/jupyter/start-notebook.sh \
resources/jupyter/start-singleuser.sh \
/usr/local/bin/
# Configure Jupyter / JupyterLab
# Add as jupyter system configuration
COPY resources/jupyter/nbconfig /etc/jupyter/nbconfig
COPY resources/jupyter/jupyter_notebook_config.json /etc/jupyter/
# install jupyter extensions
RUN \
# Create empty notebook configuration
mkdir -p $HOME/.jupyter/nbconfig/ && \
printf "{\"load_extensions\": {}}" > $HOME/.jupyter/nbconfig/notebook.json && \
# Activate and configure extensions
jupyter contrib nbextension install --sys-prefix && \
# nbextensions configurator
jupyter nbextensions_configurator enable --sys-prefix && \
# Configure nbdime
nbdime config-git --enable --global && \
# Activate Jupytext
jupyter nbextension enable --py jupytext --sys-prefix && \
# Enable useful extensions
jupyter nbextension enable skip-traceback/main --sys-prefix && \
# jupyter nbextension enable comment-uncomment/main && \
jupyter nbextension enable toc2/main --sys-prefix && \
jupyter nbextension enable execute_time/ExecuteTime --sys-prefix && \
jupyter nbextension enable collapsible_headings/main --sys-prefix && \
jupyter nbextension enable codefolding/main --sys-prefix && \
# Disable pydeck extension, cannot be loaded (404)
jupyter nbextension disable pydeck/extension && \
# Install and activate Jupyter Tensorboard
pip install --no-cache-dir git+https://github.com/InfuseAI/jupyter_tensorboard.git && \
jupyter tensorboard enable --sys-prefix && \
# TODO moved to configuration files = resources/jupyter/nbconfig Edit notebook config
# echo '{"nbext_hide_incompat": false}' > $HOME/.jupyter/nbconfig/common.json && \
cat $HOME/.jupyter/nbconfig/notebook.json | jq '.toc2={"moveMenuLeft": false,"widenNotebook": false,"skip_h1_title": false,"sideBar": true,"number_sections": false,"collapse_to_match_collapsible_headings": true}' > tmp.$$.json && mv tmp.$$.json $HOME/.jupyter/nbconfig/notebook.json && \
# If minimal flavor - exit here
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
# Cleanup
clean-layer.sh && \
exit 0 ; \
fi && \
# TODO: Not installed. Disable Jupyter Server Proxy
# jupyter nbextension disable jupyter_server_proxy/tree --sys-prefix && \
# Install jupyter black
jupyter nbextension install https://github.com/drillan/jupyter-black/archive/master.zip --sys-prefix && \
jupyter nbextension enable jupyter-black-master/jupyter-black --sys-prefix && \
# If light flavor - exit here
if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
# Cleanup
clean-layer.sh && \
exit 0 ; \
fi && \
# Install and activate what if tool
pip install witwidget && \
jupyter nbextension install --py --symlink --sys-prefix witwidget && \
jupyter nbextension enable --py --sys-prefix witwidget && \
# Activate qgrid
jupyter nbextension enable --py --sys-prefix qgrid && \
# TODO: Activate Colab support
# jupyter serverextension enable --py jupyter_http_over_ws && \
# Activate Voila Rendering
# currently not working jupyter serverextension enable voila --sys-prefix && \
# Enable ipclusters
ipcluster nbextension enable && \
# Fix permissions? fix-permissions.sh $CONDA_ROOT && \
# Cleanup
clean-layer.sh
# install jupyterlab
RUN \
# without es6-promise some extension builds fail
npm install -g es6-promise && \
# define alias command for jupyterlab extension installs with log prints to stdout
jupyter lab build && \
lab_ext_install='jupyter labextension install -y --debug-log-path=/dev/stdout --log-level=WARN --minimize=False --no-build' && \
# jupyterlab installed in requirements section
$lab_ext_install @jupyter-widgets/jupyterlab-manager && \
# If minimal flavor - do not install jupyterlab extensions
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
# Final build with minimization
jupyter lab build -y --debug-log-path=/dev/stdout --log-level=WARN && \
# Cleanup
jupyter lab clean && \
jlpm cache clean && \
rm -rf $CONDA_ROOT/share/jupyter/lab/staging && \
clean-layer.sh && \
exit 0 ; \
fi && \
$lab_ext_install @jupyterlab/toc && \
# install temporarily from gitrepo due to the issue that jupyterlab_tensorboard does not work with 3.x yet as described here: https://github.com/chaoleili/jupyterlab_tensorboard/issues/28#issuecomment-783594541
#$lab_ext_install jupyterlab_tensorboard && \
pip install git+https://github.com/chaoleili/jupyterlab_tensorboard.git && \
# install jupyterlab git
# $lab_ext_install @jupyterlab/git && \
pip install jupyterlab-git && \
# jupyter serverextension enable --py jupyterlab_git && \
# For Matplotlib: https://github.com/matplotlib/jupyter-matplotlib
#$lab_ext_install jupyter-matplotlib && \
# Do not install any other jupyterlab extensions
if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
# Final build with minimization
jupyter lab build -y --debug-log-path=/dev/stdout --log-level=WARN && \
# Cleanup
jupyter lab clean && \
jlpm cache clean && \
rm -rf $CONDA_ROOT/share/jupyter/lab/staging && \
clean-layer.sh && \
exit 0 ; \
fi \
# Install jupyterlab language server support
&& pip install jupyterlab-lsp==3.7.0 jupyter-lsp==1.3.0 && \
# $lab_ext_install install @krassowski/jupyterlab-lsp@2.0.8 && \
# For Plotly
$lab_ext_install jupyterlab-plotly && \
$lab_ext_install install @jupyter-widgets/jupyterlab-manager plotlywidget && \
# produces build error: jupyter labextension install jupyterlab-chart-editor && \
$lab_ext_install jupyterlab-chart-editor && \
# Install jupyterlab variable inspector - https://github.com/lckr/jupyterlab-variableInspector
pip install lckr-jupyterlab-variableinspector && \
# For holoview
# TODO: pyviz is not yet supported by the current JupyterLab version
# $lab_ext_install @pyviz/jupyterlab_pyviz && \
# Install Debugger in Jupyter Lab
# pip install --no-cache-dir xeus-python && \
# $lab_ext_install @jupyterlab/debugger && \
# Install jupyterlab code formattor - https://github.com/ryantam626/jupyterlab_code_formatter
$lab_ext_install @ryantam626/jupyterlab_code_formatter && \
pip install jupyterlab_code_formatter && \
jupyter serverextension enable --py jupyterlab_code_formatter \
# Final build with minimization
&& jupyter lab build -y --debug-log-path=/dev/stdout --log-level=WARN && \
jupyter lab build && \
# Cleanup
# Clean jupyter lab cache: https://github.com/jupyterlab/jupyterlab/issues/4930
jupyter lab clean && \
jlpm cache clean && \
# Remove build folder -> should be remove by lab clean as well?
rm -rf $CONDA_ROOT/share/jupyter/lab/staging && \
clean-layer.sh
# Install Jupyter Tooling Extension
COPY resources/jupyter/extensions $RESOURCES_PATH/jupyter-extensions
RUN \
pip install --no-cache-dir $RESOURCES_PATH/jupyter-extensions/tooling-extension/ && \
# Cleanup
clean-layer.sh
# Install and activate ZSH
COPY resources/tools/oh-my-zsh.sh $RESOURCES_PATH/tools/oh-my-zsh.sh
RUN \
# Install ZSH
/bin/bash $RESOURCES_PATH/tools/oh-my-zsh.sh --install && \
# Make zsh the default shell
# Initialize conda for command line activation
# TODO do not activate for now, opening the bash shell is a bit slow
# conda init bash && \
conda init zsh && \
chsh -s $(which zsh) $NB_USER && \
# Install sdkman - needs to be executed after zsh
curl -s https://get.sdkman.io | bash && \
# Cleanup
clean-layer.sh
# Install Git LFS
COPY resources/tools/git-lfs.sh $RESOURCES_PATH/tools/git-lfs.sh
RUN \
/bin/bash $RESOURCES_PATH/tools/git-lfs.sh --install && \
# Cleanup
clean-layer.sh
### VSCODE ###
# Install vscode extension
# https://github.com/cdr/code-server/issues/171
# Alternative install: /usr/local/bin/code-server --user-data-dir=$HOME/.config/Code/ --extensions-dir=$HOME/.vscode/extensions/ --install-extension ms-python-release && \
RUN \
SLEEP_TIMER=25 && \
# If minimal flavor -> exit here
if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
exit 0 ; \
fi && \
cd $RESOURCES_PATH && \
mkdir -p $HOME/.vscode/extensions/ && \
# Install vs code jupyter - required by python extension
VS_JUPYTER_VERSION="2021.6.832593372" && \
wget --retry-on-http-error=429 --waitretry 15 --tries 5 --no-verbose https://marketplace.visualstudio.com/_apis/public/gallery/publishers/ms-toolsai/vsextensions/jupyter/$VS_JUPYTER_VERSION/vspackage -O ms-toolsai.jupyter-$VS_JUPYTER_VERSION.vsix && \
bsdtar -xf ms-toolsai.jupyter-$VS_JUPYTER_VERSION.vsix extension && \
rm ms-toolsai.jupyter-$VS_JUPYTER_VERSION.vsix && \
mv extension $HOME/.vscode/extensions/ms-toolsai.jupyter-$VS_JUPYTER_VERSION && \
sleep $SLEEP_TIMER && \
# Install python extension - (newer versions are 30MB bigger)
VS_PYTHON_VERSION="2021.5.926500501" && \
wget --no-verbose https://github.com/microsoft/vscode-python/releases/download/$VS_PYTHON_VERSION/ms-python-release.vsix && \
bsdtar -xf ms-python-release.vsix extension && \
rm ms-python-release.vsix && \
mv extension $HOME/.vscode/extensions/ms-python.python-$VS_PYTHON_VERSION && \
# && code-server --install-extension ms-python.python@$VS_PYTHON_VERSION \
sleep $SLEEP_TIMER && \
# If light flavor -> exit here
if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
exit 0 ; \
fi && \
# Install prettie: https://github.com/prettier/prettier-vscode/releases
PRETTIER_VERSION="6.4.0" && \
wget --no-verbose https://github.com/prettier/prettier-vscode/releases/download/v$PRETTIER_VERSION/prettier-vscode-$PRETTIER_VERSION.vsix && \
bsdtar -xf prettier-vscode-$PRETTIER_VERSION.vsix extension && \
rm prettier-vscode-$PRETTIER_VERSION.vsix && \
mv extension $HOME/.vscode/extensions/prettier-vscode-$PRETTIER_VERSION.vsix && \
# Install code runner: https://github.com/formulahendry/vscode-code-runner/releases/latest
VS_CODE_RUNNER_VERSION="0.9.17" && \
wget --no-verbose https://github.com/formulahendry/vscode-code-runner/releases/download/$VS_CODE_RUNNER_VERSION/code-runner-$VS_CODE_RUNNER_VERSION.vsix && \
bsdtar -xf code-runner-$VS_CODE_RUNNER_VERSION.vsix extension && \
rm code-runner-$VS_CODE_RUNNER_VERSION.vsix && \
mv extension $HOME/.vscode/extensions/code-runner-$VS_CODE_RUNNER_VERSION && \
# && code-server --install-extension formulahendry.code-runner@$VS_CODE_RUNNER_VERSION \
sleep $SLEEP_TIMER && \
# Install ESLint extension: https://marketplace.visualstudio.com/items?itemName=dbaeumer.vscode-eslint
VS_ESLINT_VERSION="2.1.23" && \
wget --retry-on-http-error=429 --waitretry 15 --tries 5 --no-verbose https://marketplace.visualstudio.com/_apis/public/gallery/publishers/dbaeumer/vsextensions/vscode-eslint/$VS_ESLINT_VERSION/vspackage -O dbaeumer.vscode-eslint.vsix && \
# && wget --no-verbose https://github.com/microsoft/vscode-eslint/releases/download/$VS_ESLINT_VERSION-insider.2/vscode-eslint-$VS_ESLINT_VERSION.vsix -O dbaeumer.vscode-eslint.vsix && \
bsdtar -xf dbaeumer.vscode-eslint.vsix extension && \
rm dbaeumer.vscode-eslint.vsix && \
mv extension $HOME/.vscode/extensions/dbaeumer.vscode-eslint-$VS_ESLINT_VERSION.vsix && \
# && code-server --install-extension dbaeumer.vscode-eslint@$VS_ESLINT_VERSION \
# Fix permissions
fix-permissions.sh $HOME/.vscode/extensions/ && \
# Cleanup
clean-layer.sh
### END VSCODE ###
### INCUBATION ZONE ###
RUN \
apt-get update && \
# Required by magenta
# apt-get install -y libasound2-dev && \
# required by rodeo ide (8MB)
# apt-get install -y libgconf2-4 && \
# required for pvporcupine (800kb)
# apt-get install -y portaudio19-dev && \
# Audio drivers for magenta? (3MB)
# apt-get install -y libasound2-dev libjack-dev && \
# libproj-dev required for cartopy (15MB)
# apt-get install -y libproj-dev && \
# mysql server: 150MB
# apt-get install -y mysql-server && \
# If minimal or light flavor -> exit here
if [ "$WORKSPACE_FLAVOR" = "minimal" ] || [ "$WORKSPACE_FLAVOR" = "light" ]; then \
# Cleanup
clean-layer.sh && \
exit 0 ; \
fi && \
# Install fkill-cli program TODO: 30MB, remove?
# npm install --global fkill-cli && \
# Activate pretty-errors
# python -m pretty_errors -u -p && \
# Cleanup
clean-layer.sh
### END INCUBATION ZONE ###
### CONFIGURATION ###
# Copy files into workspace
COPY \
resources/docker-entrypoint.py \
resources/5xx.html \
$RESOURCES_PATH/
# Copy scripts into workspace
COPY resources/scripts $RESOURCES_PATH/scripts
# Create Desktop Icons for Tooling
COPY resources/branding $RESOURCES_PATH/branding
# Configure Home folder (e.g. xfce)
COPY resources/home/ $HOME/
# Copy some configuration files
COPY resources/ssh/ssh_config resources/ssh/sshd_config /etc/ssh/
COPY resources/nginx/nginx.conf /etc/nginx/nginx.conf
COPY resources/config/xrdp.ini /etc/xrdp/xrdp.ini
# Configure supervisor process
COPY resources/supervisor/supervisord.conf /etc/supervisor/supervisord.conf
# Copy all supervisor program definitions into workspace
COPY resources/supervisor/programs/ /etc/supervisor/conf.d/
# Assume yes to all apt commands, to avoid user confusion around stdin.
COPY resources/config/90assumeyes /etc/apt/apt.conf.d/
# Monkey Patching novnc: Styling and added clipboard support. All changed sections are marked with CUSTOM CODE
COPY resources/novnc/ $RESOURCES_PATH/novnc/
RUN \
## create index.html to forward automatically to `vnc.html`
# Needs to be run after patching
ln -s $RESOURCES_PATH/novnc/vnc.html $RESOURCES_PATH/novnc/index.html
# Basic VNC Settings - no password
ENV \
VNC_PW=vncpassword \
VNC_RESOLUTION=1600x900 \
VNC_COL_DEPTH=24
# Add tensorboard patch - use tensorboard jupyter plugin instead of the actual tensorboard magic
COPY resources/jupyter/tensorboard_notebook_patch.py $CONDA_PYTHON_DIR/site-packages/tensorboard/notebook.py
# Additional jupyter configuration
COPY resources/jupyter/jupyter_notebook_config.py /etc/jupyter/
COPY resources/jupyter/sidebar.jupyterlab-settings $HOME/.jupyter/lab/user-settings/@jupyterlab/application-extension/
COPY resources/jupyter/plugin.jupyterlab-settings $HOME/.jupyter/lab/user-settings/@jupyterlab/extensionmanager-extension/
COPY resources/jupyter/ipython_config.py /etc/ipython/ipython_config.py
# Branding of various components
RUN \
# Jupyter Branding
cp -f $RESOURCES_PATH/branding/logo.png $CONDA_PYTHON_DIR"/site-packages/notebook/static/base/images/logo.png" && \
cp -f $RESOURCES_PATH/branding/favicon.ico $CONDA_PYTHON_DIR"/site-packages/notebook/static/base/images/favicon.ico" && \
cp -f $RESOURCES_PATH/branding/favicon.ico $CONDA_PYTHON_DIR"/site-packages/notebook/static/favicon.ico" && \
# Fielbrowser Branding
mkdir -p $RESOURCES_PATH"/filebrowser/img/icons/" && \
cp -f $RESOURCES_PATH/branding/favicon.ico $RESOURCES_PATH"/filebrowser/img/icons/favicon.ico" && \
cp -f $RESOURCES_PATH/branding/favicon.ico $RESOURCES_PATH"/filebrowser/img/icons/favicon-32x32.png" && \