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
If you are developing and want to expose the database for inspection through a program like Sequel Pro, run:
docker compose -f docker-compose.yml -f open-db-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
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!
Known issues
Loading other seed databases
hg38 support
To enable hg38 support. First delete any existing databases and containers:
docker compose down -v
Then run
init_hg38.sh
Followed by:
docker compose up
When loading hg38 data make sure to set reference_genome: hg38 in meta_study.txt. The example study in study/ is hg19 based.
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
A different version of cBioPortal can be run using docker compose by declaring the DOCKER_IMAGE_CBIOPORTAL
environmental variable. This variable can point a DockerHub image like so:
export DOCKER_IMAGE_CBIOPORTAL=cbioportal/cbioportal:3.1.0
docker compose up
which will start the v3.1.0 portal version rather than the newer default version.
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").