cBioPortal Docker Image

This Image is based on cBioPortal (https://github.com/cBioPortal/cbioportal). It hosts the cBioPortal Backend, Frontend and a MySQL Database in a single Docker Container. The Database gets set up with the cBioPortal schema and seed data (https://github.com/cBioPortal/datahub/tree/master/seedDB), as well as common genesets (https://github.com/cBioPortal/datahub/tree/master/reference_data/gene_panels). You can import your own data into cBioPortal by providing a directory with the studies you want to import. It also hosts a loading page that redirects you to the application once its finished importing.

Building and Running the cBioPortal Docker Container

1. Build the Docker Image:

docker build -t cbioportal .

This can take a long time to complete, as it will download and build all the dependencies required to run the cBioPortal application.

2. Prepare the import directory:

To import data into cBioPortal you need to provide a directory with the following two subdirectories (gene_panels is optional):

• studies (you should put all study directories that you want to import here)
• gene_panels (incase your studies need special gene panels, you can put them here directly to import them)

The importTest directory provided in this repo contains a few working sample studies downloaded from the official cBioPortal website.

3. Run the Docker Container:

docker run -v /path/to/import/volume:/import -p 80:80 cbioportal

This will start the cBioPortal application and import all studies/genesets from the mounted /import directory.

4. Open the application:

http://localhost:80

You will first be greeted with a loading screen, as the application is still importing the data / starting up. Once the import is complete, you will be redirected to the cBioPortal homepage.

Using it in your Galaxy instance

1. Copy the tool

Copy "interactivetool_cbioportal.xml" into galaxy/tools/interactive

2. Update tool config

Update your tool config under galaxy/config/tool_conf.xml to include cbioportal under the Interactive Tool section like this:

<section id="interactivetools" name="Interactive Tools">
    <tool file="interactive/interactivetool_cbioportal.xml" />
</section>