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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 using a Docker image all dependencies for cBioPortal are included, 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

# Download the image and start a container
docker run -d --restart=always \
--name=cbioportal-container \
--net=cbio-net \
-e CATALINA_OPTS='-Xms2g -Xmx4g' \
-p 8081:8080 \
thehyve/cbioportal:1.11.3

 

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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