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Welcome

Welcome to the cBioPortal Wiki home page. This wiki contains documentation on how to deploy and administrate cBioPortal.

Helpful Pages

To deploy cBioPortal, refer to the page on Deploying cBioPortal.

To connect to server and the cBioPortal database, refer to the page on Connecting to the Database.

To add new users to the database or how to disable a user account, refer to the page on Adding Users.

To authorise a user to be able to view a study, refer to the page on Authorising Users.

To add pathology reports for study samples and CA125 plots for patients, refer to the page on Adding Pathology Reports and CA125 Plots.

For instructions on how to to import a data study into cBioPortal, refer to the page on Importing Study Data.

Important Notes

Code Syntax

Throughout this wiki code snippets are provided as examples of commands to execute. These commands include a terminal prompt at the start of the code to indicate the start of input, however they do not form part of the command to execute.

In this example $ is the shell terminal prompt and indicates commands to be executed when connected to the server or on a local machine. Everything following the terminal prompt $ forms the command to be executed.

$ cd cbioportal/scripts/ansible/

In this example mysql> is the MySQL terminal prompt and indicates commands to be executed when connected to the cbioportal database on the server. Everything following the terminal prompt mysql> up to and including the semicolon character ; forms the command to be executed when connected to the database.

mysql> use cbioportal;