README

Welcome to the documentation for cBioPortal! Below you can find an index of all available documentation to help you to deploy and maintain a local instance of cBioPortal, as well as information on how to upload data. Specific pages are also available for developers. For details on contributing code changes and pull-requests to cBioPortal, please see our CONTRIBUTING Doc.
We also maintain an active list of RFCs (Requests for Comments) where we describe new features and solicit community feedback.
1. General
​News​
​Frequently Asked Questions​
​About Us​
​List of RFCs​
2. cBioPortal Deployment
2.1 Deployment
​Architecture overview​
​Hardware Requirements​
2.1.1 Deploy with Docker (Recommended)
​Deploy with Docker​
​Import data with Docker​
​Example Commands​
​Authenticating and Authorizing Users using Keycloak in Docker​
2.1.2 Deploy without Docker
​Software Requirements​
​Pre-Build Steps​
​Building from Source​
​Importing the Seed Database​
​Deploying the Web Application​
​Loading a Sample Study​
2.2 Authorization and Authentication
​User Authorization​
​Authenticating Users via SAML​
​Authenticating Users via LDAP​
​Authenticating and Authorizing Users via Keycloak​
​Authenticating Users via Tokens​
2.3 Customization
​Customizing your cBioPortal Instance via portal.properties​
​More portal.properties Settings​
​Configuring Caching Behavior​
2.4 Integration with Other Webservices
​OncoKB Data Access​
3. cBioPortal Maintenance
​Updating your cBioPortal Database Scheme​
​Update genes and gene aliases​
4. Development
​Feature Development Guide​
​cBioPortal Entity-relationship Diagram​
​Build cBioPortal with a different frontend version​
​Session Service​
​Manual test cases​
​Release Procedure​
​Deployment Procedure​
5. Data Loading
5.1 Data Loading
​Data Loading Overview​
​Using the Dataset Validator​
​Using the metaImport Script​
​File Formats​
​Z-Score Normalization​
​Maintaining Studies​
​For Developers​
​Tips and Best Practices​
​Importing Gene Sets for Gene Set Scoring Data​
​Importing Gene Panels​
​Study View Customization with Priority Data​
​Importing of OncoKB annotations as custom driver annotations​
5.2 Datasets
​Downloads​
6. Web API and Clients
​API and API Clients​

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Contents

1. General

2. cBioPortal Deployment

2.1 Deployment

2.1.1 Deploy with Docker (Recommended)

2.1.2 Deploy without Docker

2.2 Authorization and Authentication

2.3 Customization

2.4 Integration with Other Webservices

3. cBioPortal Maintenance

6. Web API and Clients