dexwel / cbioportal-docker-compose

Run cBioPortal using Docker Compose

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

Macbook M1

See ticket and solution: cBioPortal/cbioportal#9829

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").