Configuration

Configuration files

There are four configuration files, all of them are written in YAML format:

1. configuration.yml: general and common configuration for different OpenCGA components
2. catalog-configuration.yml: contains the specific configuration for OpenCGA Catalog such as metadata database
3. storage-configuration.yml: contains the storage-related configuration variables to index and query data
4. client-configuration.yml: this the only configuration required for user CLI (opencga.sh) and RESTful web services clients (Java, Python, R and JavaScript)

In the next section you will find all the variables together with the Maven Property (written using italics in parenthesis) used during the building to set the default value, remember that you can set these properties using a profile in the settings.xml file or in the mvn install command line itself.

General configuration

This is general file, you find it at https://github.com/opencb/opencga/blob/develop/opencga-core/src/main/resources/configuration.yml, its configuration is used by different components, the variables are:

Option 1

• rest: these determine the REST server properties
  • port (OPENCGA.SERVER.REST.PORT):
  • defaultLimit:

Option 2

Variable	Maven property	Description
rest	-	these determine the REST server properties
rest > port	OPENCGA.SERVER.REST.PORT	set the REST server port

Option 3

Rest section

This determine the REST server properties

• port (OPENCGA.SERVER.REST.PORT):
• defaultLimit:

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Catalog configuration

This file is called catalog-configuration.yml, the variables are:

Storage configuration

Client configuration