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cBioPortal setup made easy using Docker

December 13, 2017 | By Sander Tan

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The easiest way to install cBioPortal is using Docker. The Hyve has helped a number of clients in the past with installation of cBioPortal on their infrastructure. By using a Docker image all dependencies for cBioPortal are included, and default settings to connect to the MySQL database are configured.


(These instructions have been updated for cBioPortal v2.0.1)

 

 When you have Docker installed please check the following prerequisites:

  • If you are a Linux user, add yourself to a docker group after installation.
  • Dedicate at least 4GB of memory to Docker. 

Run the following commands to start cBioPortal:

# Download the database schema and seed database
 
# Start the docker network
docker network create cbio-net
 
# Set up the database (this will take a few minutes). Please make sure the folder
# `cbioportal_database_files` does not exist yet.
docker run -d --restart=always \
    --name='cbioDB' \
    --net=cbio-net \
    -e MYSQL_ROOT_PASSWORD=P@ssword1 \
    -e MYSQL_USER=cbio \
    -e MYSQL_PASSWORD=P@ssword1 \
    -e MYSQL_DATABASE=cbioportal \
    -v $PWD'/cbioportal_database_files/':/var/lib/mysql/ \
    -v $PWD'/cgds.sql':/docker-entrypoint-initdb.d/cgds.sql:ro \
    -v $PWD'/seed-cbioportal_hg19_v2.7.3.sql.gz':/docker-entrypoint-initdb.d/seed_part1.sql.gz:ro \
    mysql:5.7
 
# If you would like to access the MySQL database from your local environment, you could map the MySQL port
# in Docker (3306) to a local port (8306) by inserting this to the docker run command: -p 8306:3306 \

It will take several minutes to start the database. Progress can be viewed with docker logs -f cbioDB. "MySQL init process done. Ready for start up.” marks the process as completed. Exit with CTRL+C. If you would like to redo this part, remove the local database folder.

# Download a default configuration file
wget https://github.com/thehyve/cbioportal-docker/raw/ed4266e1754dd0af5ceda9d7da3bc0145d75d809/portal.properties
 
# Download the image and start a container
docker run -d --restart=always \
    --name=cbioportal-container \
    --net=cbio-net \
    -v $PWD'/portal.properties':/cbioportal/portal.properties:ro \
    -e CATALINA_OPTS='-Xms2g -Xmx4g' \
    -p 8081:8080 \
    thehyve/cbioportal:v2.0.1-iss5758

cBioPortal is now running and accessible at http://localhost:8081/cbioportal/. The next step is to load a study in cBioPortal. For this you can follow the instructions in our next blogpost, which explains how to load public TCGA study from cBioPortal Data HubThe full step-by-step documentation for this process is described in our GitHub repository. This also contains instructions how to view, stop and remove containers.

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Related blog: Simple data loading into cBioPortal with Docker