The cBioPortal project documents a setup to deploy a cBioPortal server using Docker, in this section of the documentation. As cBioPortal traditionally did not distinguish between build-time and deploy-time configuration, the setup documented there builds the application at runtime, and suggests running auxiliary commands in the same container as the webserver. The above approach may sacrifice a few advantages of using Docker by going against some of its idioms. For this reason, the project you are currently looking at documents an alternative setup, which builds a ready-to-run cBioPortal application into a Docker image.
To get started, download and install Docker from www.docker.com.
Create a network in order for the cBioPortal container and mysql database to communicate.
docker network create cbio-net
Start a MySQL server. The command below stores the database in a folder named
/<path_to_save_mysql_db>/db_files/. This should be an absolute path.
docker run -d --restart=always \
--name=cbioDB \
--net=cbio-net \
-e MYSQL_ROOT_PASSWORD='P@ssword1' \
-e MYSQL_USER=cbio \
-e MYSQL_PASSWORD='P@ssword1' \
-e MYSQL_DATABASE=cbioportal \
-v /<path_to_save_mysql_db>/db_files/:/var/lib/mysql/ \
mysql:5.7
Download the seed database from the cBioPortal Datahub, and use the command below to upload the seed data to the server started above.
Make sure to replace
/<path_to_seed_database>/seed-cbioportal_<genome_build>_<seed_version>.sql.gz
with the path and name of the downloaded seed database. Again, this should be
an absolute path.
docker run \
--name=load-seeddb \
--net=cbio-net \
-e MYSQL_USER=cbio \
-e MYSQL_PASSWORD='P@ssword1' \
-v /<path_to_seed_database>/cgds.sql:/mnt/cgds.sql:ro \
-v /<path_to_seed_database>/seed-cbioportal_<genome_build>_<seed_version>.sql.gz:/mnt/seed.sql.gz:ro \
mysql:5.7 \
sh -c 'cat /mnt/cgds.sql | mysql -hcbioDB -u"$MYSQL_USER" -p"$MYSQL_PASSWORD" cbioportal \
&& zcat /mnt/seed.sql.gz | mysql -hcbioDB -u"$MYSQL_USER" -p"$MYSQL_PASSWORD" cbioportal'
Follow the logs of this step to ensure that no errors occur. If any error
occurs, make sure to check it. A common cause is pointing the -v parameters
above to folders or files that do not exist.
Run the command below to build the latest version.
docker build -t cbioportal-image https://github.com/thehyve/cbioportal-docker.git
If you want to build an image based on a different branch, you can read this.
Obtain the portal.properties.
configuration file for the Docker setup from this repository.
Update the seeded database schema to match the cBioPortal version in the image, by running the following command. Note that this will most likely make your database irreversibly incompatible with older versions of the portal code.
docker run --rm -it --net cbio-net \
-v /<path_to_config_file>/portal.properties:/cbioportal/portal.properties:ro \
cbioportal-image \
migrate_db.py -p /cbioportal/portal.properties -s /cbioportal/db-scripts/src/main/resources/migration.sql
First, create the mongoDB database:
docker run -d --name=mongoDB --net=cbio-net \
-e MONGO_INITDB_DATABASE=session_service \
mongo:4.0
Finally, create a container for the Session Service, adding the link to the mongoDB database using -Dspring.data.mongodb.uri:
docker run -d --name=cbio-session-service --net=cbio-net \
-e JAVA_OPTS="-Dspring.data.mongodb.uri=mongodb://mongoDB:27017/session-service" \
thehyve/cbioportal-session-service:cbiov2.1.0
Add any cBioPortal configuration in portal.properties as appropriate—see
the documentation on the
main properties
and the
skin properties.
Then start the web server as follows.
docker run -d --restart=always \
--name=cbioportal-container \
--net=cbio-net \
-v /<path_to_config_file>/portal.properties:/cbioportal/portal.properties:ro \
-e CATALINA_OPTS='-Xms2g -Xmx4g' \
-p 8081:8080 \
cbioportal-image
On server systems that can easily spare 4 GiB or more of memory,
set the -Xms and -Xmx options to the same number. This should
increase performance of certain memory-intensive web services such
as computing the data for the co-expression tab. If you are using
MacOS or Windows, make sure to take a look at these
notes to allocate more memory for the
virtual machine in which all Docker processes are running.
cBioPortal can now be reached at http://localhost:8081/cbioportal/
Activity of Docker containers can be seen with:
docker ps -a
For more uses of the cBioPortal image, see this file
To build images from development source rather than stable releases or snapshots, see development.md.
To Dockerize a Keycloak authentication service alongside cBioPortal, see this file.
First we stop the Docker containers.
docker stop cbioDB
docker stop cbioportal-container
Then we remove the Docker containers.
docker rm cbioDB
docker rm cbioportal-container
Cached Docker images can be seen with:
docker images
Finally we remove the cached Docker images.
docker rmi mysql:5.7
docker rmi cbioportal-image