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Dockerfile
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# Dockerfile for cBioPortal
FROM elementolab/jamm:1.0
MAINTAINER Alexandros Sigaras <[email protected]>
#===========================#
# Clone cBioPortal #
#===========================#
RUN git clone https://github.com/cBioPortal/cbioportal.git; \
cd cbioportal ; git checkout v1.2.1; \
echo "export PORTAL_HOME=/cbioportal" >> /root/.bash_profile;
#===========================#
# ADD Default Config #
#===========================#
ADD config /default_config
RUN cp default_config/* /cbioportal/src/main/resources/; \
source /root/.bash_profile; /bin/cp -u --force /default_config/context.xml $CATALINA_HOME/conf/context.xml;
#===========================#
# Build From Source #
#===========================#
ADD build /cbio_build
RUN cp cbio_build/gene_sets.txt /cbioportal/core/src/main/resources/; \
mkdir ~/.m2/; cp /cbio_build/settings.xml ~/.m2/; \
source /root/.bash_profile; cd $PORTAL_HOME; mvn -DskipTests clean install
#===========================#
# ADD Scripts #
#===========================#
ADD scripts /cbio_scripts
#===========================#
# Copy cBioPortal .war file #
#===========================#
RUN source /root/.bash_profile; \
cp $PORTAL_HOME/portal/target/cbioportal.war $CATALINA_HOME/webapps/
#===========================#
# Startup #
#===========================#
CMD /bin/bash /cbio_scripts/entrypoint.sh;
#===========================================================================================#