Configuration files

There are four

Overview

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

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
storage-configuration.yml: contains the storage-related configuration variables settings to index and query genomic data
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)

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

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 CLI and client libraries to interact with the REST or gRPC services. You can find all the configuration files in the conf folder of the OpenCGA installation.

Configuring at run time

After installing OpenCGA you will have to edit the different configuration files. You can find more information about how to do this in the pages in the section:

configuration.yml
storage-configuration.yml
client-configuration.yml

Configuring at build time with Maven

In order to make easier the deployment we have defined several Maven Properties to automatically set the values when building OpenCGA form source code. These are defined in a default Maven Profile at main OpenCGA pom.xml. Note that you can define several maven profiles at ~/.m2/settings.xml, each of these profiles can set different values for different environments, e.g. test or production cluster can have different hosts or passwords. You can easily activate one profile when building using maven -P option.:

Code Block

language	bash

mvn clean install -P PROFILE_NAME

By doing this maven will automatically substitute the maven property value in the corresponding configuration file. For example, in the client configuration file we can find the following section:

Code Block

linenumbers	true

## REST client configuration options
rest:
  host: "${OPENCGA.CLIENT.REST.HOST}"
  batchQuerySize: 200
  timeout: ${OPENCGA.CLIENT.REST.TIMEOUT}
  defaultLimit: 2000

Both OPENCGA.CLIENT.REST.HOST and OPENCGA.CLIENT.REST.TIMEOUT will be replaced for the corresponding value in the maven properties in your profile:

Code Block

linenumbers	true

<OPENCGA.CLIENT.REST.HOST>localhost:8080/opencga</OPENCGA.CLIENT.REST.HOST>
<OPENCGA.CLIENT.REST.TIMEOUT>30000</OPENCGA.CLIENT.REST.TIMEOUT>

The names of the Maven properties have been designed to indicate in which file the property will be injected. Properties starting with OPENCGA.STORAGE will go to storage-configuration.yml while properties starting with OPENCGA.CLIENT will go to client-configuration.yml. The rest of the properties go to configuration.yml.

At this moment this is the default profile at main pom.xml file:

Code Block

language	xml
title	Maven Default Profile
linenumbers	true

<profile>
    <id>default-config</id>
    <activation>
        <activeByDefault>true</activeByDefault>
    </activation>
    <properties>
        <opencga.war.name>opencga-${opencga.version}</opencga.war.name>

        <!-- General -->
        <OPENCGA.INSTALLATION.DIR>/opt/opencga</OPENCGA.INSTALLATION.DIR>
        <OPENCGA.USER.WORKSPACE>/opt/opencga/sessions</OPENCGA.USER.WORKSPACE>
        <OPENCGA.JOBS.DIR>${OPENCGA.USER.WORKSPACE}/jobs</OPENCGA.JOBS.DIR>
        <OPENCGA.TOOLS.DIR>${OPENCGA.INSTALLATION.DIR}/tools</OPENCGA.TOOLS.DIR>
        <OPENCGA.DB.PREFIX>opencga</OPENCGA.DB.PREFIX>
        <OPENCGA.EXECUTION.MODE>LOCAL</OPENCGA.EXECUTION.MODE>

        <!-- Client -->
        <OPENCGA.CLIENT.REST.HOST>http://localhost:8080/${opencga.war.name}</OPENCGA.CLIENT.REST.HOST>
        <OPENCGA.CLIENT.REST.TIMEOUT>30000</OPENCGA.CLIENT.REST.TIMEOUT>
        <OPENCGA.CLIENT.GRPC.HOST>localhost:9091</OPENCGA.CLIENT.GRPC.HOST>
        <OPENCGA.CLIENT.ORGANISM.SCIENTIFIC_NAME></OPENCGA.CLIENT.ORGANISM.SCIENTIFIC_NAME>
        <OPENCGA.CLIENT.ORGANISM.COMMON_NAME></OPENCGA.CLIENT.ORGANISM.COMMON_NAME>
        <OPENCGA.CLIENT.ORGANISM.TAXONOMY_CODE></OPENCGA.CLIENT.ORGANISM.TAXONOMY_CODE>
        <OPENCGA.CLIENT.ORGANISM.ASSEMBLY></OPENCGA.CLIENT.ORGANISM.ASSEMBLY>

        <OPENCGA.SERVER.REST.PORT>9090</OPENCGA.SERVER.REST.PORT>
        <OPENCGA.SERVER.GRPC.PORT>9091</OPENCGA.SERVER.GRPC.PORT>
        <OPENCGA.MONITOR.PORT>9092</OPENCGA.MONITOR.PORT>

        <!-- Catalog -->
        <OPENCGA.CATALOG.DB.HOSTS>localhost:27017</OPENCGA.CATALOG.DB.HOSTS>
        <OPENCGA.CATALOG.DB.USER></OPENCGA.CATALOG.DB.USER>
        <OPENCGA.CATALOG.DB.PASSWORD></OPENCGA.CATALOG.DB.PASSWORD>
        <OPENCGA.CATALOG.DB.AUTHENTICATION_DATABASE></OPENCGA.CATALOG.DB.AUTHENTICATION_DATABASE>
        <OPENCGA.CATALOG.DB.CONNECTIONS_PER_HOST>20</OPENCGA.CATALOG.DB.CONNECTIONS_PER_HOST>

        <!-- Storage -->
        <OPENCGA.STORAGE.DEFAULT_ENGINE>mongodb</OPENCGA.STORAGE.DEFAULT_ENGINE>
        <OPENCGA.STORAGE.CACHE.HOST>localhost:6379</OPENCGA.STORAGE.CACHE.HOST>
        <OPENCGA.STORAGE.SEARCH.HOST>http://localhost:8983/solr/</OPENCGA.STORAGE.SEARCH.HOST>
        <OPENCGA.STORAGE.SEARCH.TIMEOUT>30000</OPENCGA.STORAGE.SEARCH.TIMEOUT>
        <OPENCGA.STORAGE.SEARCH.HOST>http://bioinfodev.hpc.cam.ac.uk/solr/</OPENCGA.STORAGE.SEARCH.HOST>

        <!-- Storage Variants general -->
        <OPENCGA.STORAGE.VARIANT.DB.HOSTS>localhost:27017</OPENCGA.STORAGE.VARIANT.DB.HOSTS>
        <OPENCGA.STORAGE.VARIANT.DB.USER></OPENCGA.STORAGE.VARIANT.DB.USER>
        <OPENCGA.STORAGE.VARIANT.DB.PASSWORD></OPENCGA.STORAGE.VARIANT.DB.PASSWORD>

        <!-- Storage Alignments general -->
        <OPENCGA.STORAGE.ALIGNMENT.DB.HOSTS>localhost:27017</OPENCGA.STORAGE.ALIGNMENT.DB.HOSTS>
        <OPENCGA.STORAGE.ALIGNMENT.DB.USER></OPENCGA.STORAGE.ALIGNMENT.DB.USER>
        <OPENCGA.STORAGE.ALIGNMENT.DB.PASSWORD></OPENCGA.STORAGE.ALIGNMENT.DB.PASSWORD>

        <!-- Storage-mongodb -->
        <OPENCGA.STORAGE.MONGODB.VARIANT.DB.AUTHENTICATION_DATABASE></OPENCGA.STORAGE.MONGODB.VARIANT.DB.AUTHENTICATION_DATABASE>
        <OPENCGA.STORAGE.MONGODB.VARIANT.DB.CONNECTIONS_PER_HOST>20</OPENCGA.STORAGE.MONGODB.VARIANT.DB.CONNECTIONS_PER_HOST>

        <!-- Storage-hadoop -->
        <!--If empty, will use the ZOOKEEPER_QUORUM read from the hbase configuration files-->
        <OPENCGA.STORAGE.HADOOP.VARIANT.DB.HOSTS></OPENCGA.STORAGE.HADOOP.VARIANT.DB.HOSTS>
        <OPENCGA.STORAGE.HADOOP.VARIANT.DB.USER></OPENCGA.STORAGE.HADOOP.VARIANT.DB.USER>
        <OPENCGA.STORAGE.HADOOP.VARIANT.DB.PASSWORD></OPENCGA.STORAGE.HADOOP.VARIANT.DB.PASSWORD>
        <OPENCGA.STORAGE.HADOOP.VARIANT.HBASE.NAMESPACE></OPENCGA.STORAGE.HADOOP.VARIANT.HBASE.NAMESPACE>
        <OPENCGA.STORAGE.HADOOP.VARIANT.ARCHIVE.TABLE.PREFIX>${OPENCGA.DB.PREFIX}_study</OPENCGA.STORAGE.HADOOP.VARIANT.ARCHIVE.TABLE.PREFIX>

        <!-- Email server -->
        <OPENCGA.MAIL.HOST></OPENCGA.MAIL.HOST>
        <OPENCGA.MAIL.PORT></OPENCGA.MAIL.PORT>
        <OPENCGA.MAIL.USER></OPENCGA.MAIL.USER>
        <OPENCGA.MAIL.PASSWORD></OPENCGA.MAIL.PASSWORD>

        <!-- cellbase -->
        <OPENCGA.CELLBASE.VERSION>v4</OPENCGA.CELLBASE.VERSION>
        <OPENCGA.CELLBASE.REST.HOST>http://bioinfo.hpc.cam.ac.uk/cellbase/</OPENCGA.CELLBASE.REST.HOST>
        <OPENCGA.CELLBASE.DB.HOST>localhost:27017</OPENCGA.CELLBASE.DB.HOST>
        <OPENCGA.CELLBASE.DB.USER></OPENCGA.CELLBASE.DB.USER>
        <OPENCGA.CELLBASE.DB.PASSWORD></OPENCGA.CELLBASE.DB.PASSWORD>
        <OPENCGA.CELLBASE.DB.AUTHENTICATION_DATABASE></OPENCGA.CELLBASE.DB.AUTHENTICATION_DATABASE>
        <OPENCGA.CELLBASE.DB.READ_PREFERENCE>secondaryPreferred</OPENCGA.CELLBASE.DB.READ_PREFERENCE>
    </properties>
</profile>

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Old Version 2

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Key

Configuration files

Overview

General configuration

Variable | Maven property | Description

Catalog configuration

Storage configuration

Configuring at run time

Configuring at build time with Maven

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Page History

Versions Compared

Old Version 2

New Version Current

Key

Configuration files

Overview

General configuration

Variable | Maven property | Description

Catalog configuration

Storage configuration

Configuring at run time

Configuring at build time with Maven