Deploy with Docker

Prerequisites

Docker provides a way to run applications securely isolated in a container, packaged with all its dependencies and libraries. To learn more on Docker, kindly refer here: What is Docker?.

Make sure that you have the latest version of Docker installed on your machine. Get latest version

Notes for non-Linux systems

Usage instructions

Step 1 - Setup network

Create a network in order for the cBioPortal container and mysql database to communicate.

docker network create cbio-net

Step 2 - Run mysql with seed database

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.

Note that another option would be to use an external database. In that case one does not need to run the cbioDB container. In the command for the load-seeddb change the cbioDB host to the host of the external MySQL database.

Step 3 - Set up a portal.properties file

Copy the portal.properties.EXAMPLE and change it according to your wishes. See the full reference and the skin properties for more information on the relevant properties.

Make sure to at least provide the database parameters from step 1, which are required for the next step:

db.user=cbio
db.password=P@ssword1
db.host=cbioDB
db.portal_db_name=cbioportal
db.connection_string=jdbc:mysql://cbioDB/

If you are using an external database change the cbioDB hostname to the hostname of the MySQL database. If it requires an SSL connection use:

db.use_ssl=true

Step 4 - Migrate database to latest version

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/cbioportal:3.0.1 \
migrate_db.py -p /cbioportal/portal.properties -s /cbioportal/db-scripts/src/main/resources/migration.sql

Step 5 - Run Session Service containers

First, create the mongoDB database:

docker run -d --name=mongoDB --net=cbio-net \
-e MONGO_INITDB_DATABASE=session_service \
mongo:3.6.6

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 SERVER_PORT=5000 \
-e JAVA_OPTS="-Dspring.data.mongodb.uri=mongodb://mongoDB:27017/session-service" \
cbioportal/session-service:latest

Step 6 - Run the cBioPortal web server

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 JAVA_OPTS='
-Xms2g
-Xmx4g
-Dauthenticate=noauthsessionservice
-Dsession.service.url=http://cbio-session-service:5000/api/sessions/my_portal/
' \
-p 8081:8080 \
cbioportal/cbioportal:3.0.1 \
/bin/sh -c 'java ${JAVA_OPTS} -jar webapp-runner.jar /cbioportal-webapp'

To read more about the various ways to use authentication and webapp-runner see the relevant backend deployment documentation.

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/

Activity of Docker containers can be seen with:

docker ps -a

Data loading & more commands

For more uses of the cBioPortal image, see this file

To Dockerize a Keycloak authentication service alongside cBioPortal, see this file.

Uninstalling cBioPortal

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 mongo:3.6.6