Run cBioPortal using Docker Compose

Download necessary files (seed data, example config and example study from datahub):

./init.sh

Start docker containers. This can take a few minutes the first time because the database needs to import some data.

docker compose up

The cbioportal application should now be running at localhost:8080, with the one of the studies already loaded in it.

If you are developing and want to expose the MySQL database for inspection through a program like Sequel Pro, run:

docker compose -f docker-compose.yml -f dev/open-ports.yml up

In a different terminal import a study

docker-compose exec cbioportal metaImport.py -u http://cbioportal:8080 -s study/lgg_ucsf_2014/ -o

The example study in the study/ directory is based on hg19. When importing hg38 data, be sure to set reference_genome: hg38 in the meta_study.txt.

Restart the cbioportal container after importing

docker-compose restart cbioportal

The compose file uses docker volumes which persist data between reboots. To completely remove all data run:

docker compose down -v

If you were able to successfully set up a local installation of cBioPortal, please add it here: https://www.cbioportal.org/installations. Thank you!

Clickhouse Mode

For cBioPortal instances with large cohorts (>100K samples), we developed a "Clickhouse mode" of the Study View. This mode uses Clickhouse as an additional database next to MySQL for 10x faster querying (see video). The mode is experimental and is currently used only by the public-facing GENIE instance. We plan to roll it out to other portals later this year (see roadmap ticket). Follow the steps below to run cBioPortal Docker Compose in clickhouse mode.

1. Modify .env to use clickhouse-compatible release of cBioPortal.

   ...
   DOCKER_IMAGE_CBIOPORTAL=cbioportal/cbioportal:6.0.27
   ...
   

2. Run init script

   ./init.sh

3. Start cBioPortal with clickhouse

   docker compose -f docker-compose.yml -f addon/clickhouse/docker-compose.clickhouse.yml up

Clickhouse Cloud

The Clickhouse setup mentioned above is fully compatible with a remote Clickhouse database. For production environments, you can set up a Clickhouse database using Clickhouse Cloud and update the clickhouse database credentials in the .env to match your database credentials. For the clickhouse sync step to work properly, your credentials should have both read and write permissions.

Example Commands

Connect to the database

docker compose exec cbioportal-database \
    sh -c 'mysql -hcbioportal-database -u"$MYSQL_USER" -p"$MYSQL_PASSWORD" "$MYSQL_DATABASE"'

Advanced topics

Run different cBioPortal version

This cBioPortal Docker Compose setup runs the latest release of cBioPortal. If you want to run more recent pre-releases, follow the steps below:

1. Modify DOCKER_IMAGE_CBIOPORTAL environmental variable to point to a valid cBioPortal Docker Image.

   export DOCKER_IMAGE_CBIOPORTAL=cbioportal/cbioportal:6.2.0
   

2. Restart cbioportal

   docker compose restart cbioportal

Run the 'web-shenandoah' cBioPortal image

A web-only version of cBioPortal (suffixed -web-shenandoah) can be run using docker compose by declaring the DOCKER_IMAGE_CBIOPORTAL environmental variable to point to the corresponding image:

export DOCKER_IMAGE_CBIOPORTAL=cbioportal/cbioportal:6.0.20-web-shenandoah
docker compose -f docker-compose.yml -f dev/docker-compose.web.yml up

which will start the v6.0.20-web-shenandoah version rather than the newest default version.

Keycloak Authentication

To set up a keycloak server with your cBioPortal instance for development purposes, check out the documentation.

Change the heap size

Web app

You can change the heap size in the command section of the cbioportal container

Importer

For the importer you can't directly edit the java command used to import a study. Instead add JAVA_TOOL_OPTIONS as an environment variable to the cbioportal container and set the desired JVM parameters there (e.g. JAVA_TOOL_OPTIONS: "-Xms4g -Xmx8g").