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Dockerfile
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#Download base image ubuntu
FROM ubuntu:20.04
ENV DEBIAN_FRONTEND noninteractive
ENV LC_CTYPE en_US.UTF-8
ENV LANG en_US.UTF-8
ENV R_BASE_VERSION 3.6.1
LABEL maintainer "Alberto Santos alberto.santos@sund.ku.dk"
USER root
RUN apt-get update && \
apt-get -yq dist-upgrade && \
apt-get install -yq --no-install-recommends && \
apt-get install -yq apt-utils software-properties-common && \
apt-get install -yq locales && \
apt-get install -yq wget && \
apt-get install -yq unzip && \
apt-get install -yq build-essential sqlite3 libsqlite3-dev libxml2 libxml2-dev zlib1g-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev libreadline-dev libffi-dev libcurl4-openssl-dev && \
apt-get install -yq nginx && \
apt-get install -yq redis-server && \
apt-get install -y dos2unix && \
apt-get install -yq git && \
apt-get install -y sudo && \
apt-get install -y net-tools &&\
rm -rf /var/lib/apt/lists/*
# User management
RUN groupadd ckg_group && \
adduser --quiet --disabled-password --shell /bin/bash --home /home/adminhub --gecos "User" adminhub && \
echo "adminhub:adminhub" | chpasswd && \
usermod -a -G ckg_group adminhub && \
adduser --quiet --disabled-password --shell /bin/bash --home /home/ckguser --gecos "User" ckguser && \
echo "ckguser:ckguser" | chpasswd && \
usermod -a -G ckg_group ckguser && \
adduser --disabled-password --gecos '' --uid 1500 nginx && \
usermod -a -G ckg_group nginx
RUN wget https://www.python.org/ftp/python/3.7.9/Python-3.7.9.tgz
RUN tar -xzf Python-3.7.9.tgz
WORKDIR /Python-3.7.9
RUN ./configure
RUN make altinstall
RUN make install
## pip upgrade
RUN wget https://bootstrap.pypa.io/get-pip.py
RUN python3 get-pip.py
RUN pip3 install --upgrade pip
RUN pip3 install setuptools
WORKDIR /
# Set the locale
RUN locale-gen en_US.UTF-8
# gpg key for cran updates
RUN gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E084DAB9 && \
gpg -a --export E084DAB9 > cran.asc && \
apt-key add cran.asc
RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 51716619E084DAB9
RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" > /etc/apt/sources.list.d/cran.list
# Installation openJDK 11
RUN add-apt-repository ppa:openjdk-r/ppa
RUN apt-get update
RUN apt-get install -yq openjdk-11-jdk
RUN java -version
RUN javac -version
# NEO4J 4.2.3
RUN wget -O - https://debian.neo4j.com/neotechnology.gpg.key | apt-key add - && \
echo "deb [trusted=yes] https://debian.neo4j.com stable 4.2" > /etc/apt/sources.list.d/neo4j.list && \
apt-get update && \
apt-get install -yq neo4j=1:4.2.3
## Setup initial user Neo4j
RUN rm -f /var/lib/neo4j/data/dbms/auth && \
neo4j-admin set-initial-password "NeO4J"
## Install graph data science library and APOC
RUN wget -P /var/lib/neo4j/plugins https://github.com/neo4j/graph-data-science/releases/download/1.5.1/neo4j-graph-data-science-1.5.1.jar
RUN wget -P /var/lib/neo4j/plugins https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/4.2.0.4/apoc-4.2.0.4-all.jar
## Change configuration
COPY /resources/neo4j_db/neo4j.conf /etc/neo4j/.
RUN dos2unix /etc/neo4j/neo4j.conf
## Test the service Neo4j
RUN service neo4j start && \
sleep 60 && \
ls -lrth /var/log && \
service neo4j stop
# Load backup with Clinical Knowledge Graph
RUN mkdir -p /var/lib/neo4j/data/backup
RUN wget -O /var/lib/neo4j/data/backup/ckg_latest_4.2.3.dump https://datashare.biochem.mpg.de/s/kCW7uKZYTfN8mwg/download
RUN mkdir -p /var/lib/neo4j/data/databases/graph.db
RUN sudo -u neo4j neo4j-admin load --from=/var/lib/neo4j/data/backup/ckg_latest_4.2.3.dump --database=graph.db --force
# # Remove dump file
RUN echo "Done with restoring backup, removing backup folder"
RUN rm -rf /var/lib/neo4j/data/backup
RUN [ -e /var/lib/neo4j/data/databases/store_lock ] && rm /var/lib/neo4j/data/databases/store_lock
#R
RUN apt-get update && \
apt-get install -y --no-install-recommends \
littler \
r-cran-littler \
r-base=${R_BASE_VERSION}* \
r-base-dev=${R_BASE_VERSION}* \
r-recommended=${R_BASE_VERSION}* && \
echo 'options(repos = c(CRAN = "https://cloud.r-project.org/"), download.file.method = "libcurl")' >> /etc/R/Rprofile.site
## Install packages
COPY /resources/R_packages.R /R_packages.R
RUN Rscript R_packages.R
# CKG Python library
COPY ./requirements.txt .
## Install Python libraries
RUN python3 -m pip install --ignore-installed -r requirements.txt
###Creating CKG directory and setting up CKG
RUN mkdir /CKG
COPY --chown=nginx ckg /CKG/ckg
COPY data /CKG/data
RUN wget -O /CKG/data.zip https://datashare.biochem.mpg.de/s/fP6MKhLRfceWwxC/download
RUN unzip /CKG/data.zip -d /CKG/.
RUN chown -R nginx /CKG/data
COPY docker_entrypoint.sh /CKG/.
ENV PYTHONPATH "${PYTHONPATH}:/CKG"
RUN ls -lrth /CKG
### Installation
WORKDIR /CKG
RUN python3 ckg/init.py
RUN touch log/graphdb_builder.log log/graphdb_connector.log log/report_manager.log log/analytics_factory.log
#### Directory ownership
RUN chown -R nginx .
RUN chgrp -R ckg_group .
RUN chmod 777 log/ -R
RUN ls -alrth .
RUN ls -alrth data
WORKDIR /
# JupyterHub
RUN apt-get -y install npm nodejs && \
npm install -g configurable-http-proxy
RUN pip3 install jupyterhub
RUN mkdir /etc/jupyterhub
COPY /resources/jupyterhub.py /etc/jupyterhub/.
RUN cp -r /CKG/ckg/notebooks /home/adminhub/.
RUN cp -r /CKG/ckg/notebooks /home/ckguser/.
RUN chown -R adminhub /home/adminhub/notebooks
RUN chgrp -R adminhub /home/adminhub/notebooks
RUN chown -R ckguser /home/ckguser/notebooks
RUN chgrp -R ckguser /home/ckguser/notebooks
# NGINX and UWSGI
## Copy configuration file
COPY /resources/nginx.conf /etc/nginx/.
RUN chmod 777 /run/ -R && \
chmod 777 /root/ -R
## Install uWSGI
RUN pip3 install uwsgi
## Copy the base uWSGI ini file
COPY /resources/uwsgi.ini /etc/uwsgi/apps-available/uwsgi.ini
COPY /resources/uwsgi.ini /etc/uwsgi/apps-enabled/uwsgi.ini
## Create log directory
RUN mkdir -p /var/log/uwsgi
# Remove apt cache to make the image smaller
RUN rm -rf /var/lib/apt/lists/*
RUN chmod +x /CKG/docker_entrypoint.sh && ln -s /CKG/docker_entrypoint.sh
RUN dos2unix /CKG/docker_entrypoint.sh && apt-get --purge remove -y dos2unix && rm -rf /var/lib/apt/lists/*
# Expose ports (HTTP Neo4j, Bolt Neo4j, jupyterHub, CKG prod, CKG dev, Redis)
EXPOSE 7474 7687 8090 8050 5000 6379
ENTRYPOINT ["/bin/bash", "/CKG/docker_entrypoint.sh"]