Overview

There are four A full OpenCGA installation requires three configuration files, all of them are written in YAML format:

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

The first two files (configuration.yml and storage-configuration.yml) are needed for running the server, while the third one (client-configuration.yml) is required only by clients to interact with the REST or gRPC servers. You can find the configuration files in the conf folder of the OpenCGA installation.

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:

Catalog configuration

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

Storage configuration

Client configuration