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

In a different terminal import a study

docker-compose run 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

Loading other seed databases

hg38 support

To enable hg38 support. First delete any existing databases and containers:

docker-compose -v

Then run

init_hg38.sh

Followed by:

docker-compose up

When loading hg38 data make sure to set reference_genome_id: hg38 in meta_study.txt. The example study in study/ is hg19 based.

Example Commands

Connect to the database

docker-compose run 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.