cBioPortal

The cBioPortal for Cancer Genomics provides visualization, analysis, and download of large-scale cancer genomics data sets. For a short intro on cBioPortal, see these introductory slides.

If you would like to know how to setup a private instance of the portal and/or get set up for developing, see the documentation. For details on contributing code changes via pull requests, see our Contributing document.

If you are interested in coordinating the development of new features, please contact cbioportal@cbioportal.org or reach out on https://slack.cbioportal.org.

📘 Documentation

See https://docs.cbioportal.org

🤝 License

See LICENSE

💻 Run Backend

cBioPortal consists of several components, please read the Architecture docs to figure out what repo would be relevant to edit. If you e.g. only want to make frontend changes, one can directly edit the frontend repo instead. Read the instructions in that repo for more info on how to do frontend development. This repo only contains the backend part. Before editing the backend, it's good to read the backend code organization.

Local Development

What MySQL database to use

We recommend to set up a MySQL database using Docker Compose. It's useful to know how to do this as it allows you to import any dataset of your choice. For debugging production issues, we also have a database available with all the data on https://cbioportal.org that one can connect to directly. Please reach out on slack to get the credentials.

Command Line

If you want to run the cBioPortal web app from the command line please follow these instructions. First, we want to make sure that all ports are open for the services set up through docker compose (i.e. not just accessible to other containers within the same Docker Compose file). To do so, in the docker compose repo run:

docker compose -f docker-compose.yml -f open-ports.yml up

This should open the ports. Now we are ready to run the cBioPortal web app locally. You can compile the backend code with:


java -Xms2g -Xmx4g \
     -Dauthenticate=noauthsessionservice \
     -Dsession.service.url=http://localhost:5000/api/sessions/my_portal/ \
     -Dsession.service.origin='*' \
     -Dspring.datasource.username=cbio_user \
     -Dspring.datasource.password=somepassword \
     -Dspring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver \
     -Dspring.jpa.database-platform=org.hibernate.dialect.MySQL5InnoDBDialect \
     -Dspring.datasource.url='jdbc:mysql://cbio_user:somepassword@localhost:3306/cbioportal?useSSL=false&allowPublicKeyRetrieval=true' \
     -Dshow.civic=true \
     -Dskin.footer='' \
     -Dapp.name='my-portal' \
     -Ddbconnector=dbcp \
     -cp "$PWD:$PWD/BOOT-INF/lib/*" \
     org.cbioportal.PortalApplication

The app should now show up at http://localhost:8080.

Deploy your development image inside Docker Compose

Another option is to deploy your development image directly into the docker-compose file. First build the image like this

docker build -t cbioportal/cbioportal:my-dev-cbioportal-image -f docker/web-and-data/Dockerfile .

Then change the env file to use cbioportal/cbioportal:my-dev-cbioportal-image.

Local Development

Note: internally we have a dev database available with the public data set that one can connect to directly. Please reach out on slack to get the credentials. It is usually best to use a small test dataset, but if a copy of the production database is necessary for e.g. fixing a bug specific to production data that can be useful.

🕵️‍♀️ Debugging

If you want to attach a debugger you can change the docker-compose.yml file to include the parameters: -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005 (make sure to expose the debug port by adding 5005:5005 in the ports section of the cbioportal container). If you are running the java app outside of docker you can add the same parameters to the java command line arguments instead.

You can then use a JAVA IDE to connect to that port. E.g. in VSCode, one would add the following configuration to launch.json to connect:

{
    "version": "0.2.0",
    "configurations": [
        {
            "type": "java",
            "name": "Debug (Attach)",
            "request": "attach",
            "hostName": "localhost",
            "port": 5005,
            "projectName": "cbioportal"
        }
    ]
}

🌳 Branch Information

	main branch	upcoming release branch	later release candidate branch
Branch name	`master`	--	`rc`
Description	All bug fixes and features not requiring database migrations go here. This code is either already in production or will be released this week	Next release that requires database migrations. Thorough manual product review often takes place for this branch before release	Later releases with features that require database migrations. This is useful to allow merging in new features without affecting the upcoming release. Could be seen as a development branch, but note that only high quality pull requests are merged. That is the feature should be pretty much ready for release after merge.
Live instance	https://www.cbioportal.org / https://master.cbioportal.org	--	https://rc.cbioportal.org
Live instance version	https://www.cbioportal.org/api/info / https://master.cbioportal.org/api/info	--	https://rc.cbioportal.org/api/info
Docker Image	cbioportal/cbioportal:master	--	cbioportal/cbioportal:rc
Kubernetes Config	production / master	--	rc
Status		--	--

🚀 Releases

Release Notes on GitHub:

https://github.com/cBioPortal/cbioportal/releases

See also the cBioPortal News section for user focused release information:

https://www.cbioportal.org/news

Docker Images are available for each tag and branch:

https://hub.docker.com/repository/docker/cbioportal/cbioportal/tags

👉 Other Repos

Read the Architecture docs to see how these relate:

License

se4bio/cbioportal

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