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cBioPortal setup made easy using Docker

November 27, 2017 | By Sander Tan

cBioportalThe 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 building an image from the Dockerfile all dependencies are downloaded and installed, and default settings to connect to the MySQL database are configured.

 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.

 

Now you can run the following commands to start cBioPortal.

# Download the seed database containing the information about genes and transcripts

wget https://raw.githubusercontent.com/cBioPortal/cbioportal/v1.10.1/db-scripts/src/main/resources/cgds.sql
wget https://github.com/cBioPortal/datahub/raw/b9662010756188a18051c983b8c445dd033703a9/seedDB/seed-cbioportal_hg19_v2.4.0.sql.gz



# Start the docker network
docker network create cbio-net

# Set up the database
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_v2.4.0.sql.gz':/docker-entrypoint-initdb.d/seed_part1.sql.gz:ro \
  mysql

# Build the image and start a container
docker build -t cbioportal-image https://github.com/thehyve/cbioportal-docker.git
docker run -d --restart=always \
  --name=cbioportal-container \
  --net=cbio-net \
  -e CATALINA_OPTS='-Xms2g -Xmx4g' \
  -p 8081:8080 \
  cbioportal-image

 

cBioPortal is now running and accessible at http://localhost:8081/cbioportal/. 

The Hyve cBioportal Github repository

The next step will be to load a study in cBioPortal. For this you can follow the instructions in our repository with a public TCGA study from Datahub.

The full step-by-step documentation for this process is described in our GitHub repositoryLeave us a message there if you are running into trouble.

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