Run cBioportal Galaxy connector Docker compose

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

./init.sh

Configure the Redis cache. The example file can be used for a demo:

cp config/redis.conf.EXAMPLE config/redis.conf

Configure cBioportal. need to modify the following lines in the default application study:

persistence.cache_type=redis
cache.endpoint.api-key=<random-api-key>
redis.name=cbioportal_galaxy
redis.leader_address=redis://<redis-leader-url>:<redis-port>
redis.follower_address=redis://<redis-follower-url>:<redis-port> # Can be the same as redis.leader_address if you only have one redis cache
redis.database=0
redis.password=<redis-password>
redis.ttl_mins=10000
redis.clear_on_startup=true

redis.password must match the one in redis.conf.

In addition, the modified cbioportal-frontend need a new variable (code available here at tmr branch: https://github.com/jCHENEBY/cbioportal/tree/tmr):

export_server_url=http://<cbioportal-galaxy-connector-url>/export-to-galaxy

It should be noted that must be this specific URL cannot be the name of a Docker container, but the one used by your navigator to reach the server.

An demo ready application.properties can be used:

cp config/application.properties.EXAMPLE config/application.properties

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

docker compose up -d

Other instructions are in the official docker compose repo: https://github.com/cBioPortal/cbioportal-docker-compose

Configuration in the Docker compose

cBioportal Galaxy connector

Code can be found here: https://github.com/jCHENEBY/cbioportal-galaxy-connector

Environment variables

GALAXY_URL: URL of your Galaxy server.

CBIOPORTAL_URL: URL of your cBioportal instance.

In this example cbioportal-galaxy-connector is on the same Docker network as Galaxy and cBioportal, they are referenced by their container name.

Volume

Study directory:

• type: bind
• source: Must be the same directory mount by the cBioportal container
• target: Where the scripts will be looking for the study

cBioportal configuration:

• type: bind
• source: Must be the same cBioportal configuration file used for the cBioportal server. It is necessary for the metaImport.py script (see cbioportal-core repo)
• target: Replace the dummy application.properties

Image directory:

• type: volume
• source: image_data
• target: Where images are uploaded and made available at http://<URL_CONNECTOR>/images/<image_name>

Galaxy

Contain default tools and tools develop for this project:

• PyClone-VI (Under Variant): https://github.com/jCHENEBY/docker-galaxy-pyclone
• Plotting clonal population from PyClone-VI output: https://github.com/jCHENEBY/galaxy-tool-plot-cluster-prevalence
• Exporting raw PyClone-VI TSV output to cBioportal as a timeline: https://github.com/jCHENEBY/galaxy-tool-export-cbioportal-timeline
• Adding images as a cBioportal resource: https://github.com/jCHENEBY/galaxy-tool-export-cbioportal-image

Environment variables

EXPORT_TIMELINE_ENDPOINT: URL endpoint of the intermediary server with the endpoint UPLOAD_IMAGE_ENDPOINT: URL endpoint of the intermediary server with the endpoint CBIOPORTAL_LOAD_RESOURCE_ENDPOINT: URL endpoint of the intermediary server with the endpoint IMAGE_BASE_URL: cannot be the name of a Docker container, but the one used by your navigator to reach the image

Volume

Galaxy database: type: volume source: galaxy_data target: Path to the Galaxy database directory

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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 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

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").