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OPENCGA.CATALOG.DB.HOSTS: This property should be configured with the host and port of the MongoDB installation. By default, for development purposes, we have it set with "localhost:27017".
OPENCGA.CATALOG.DB.DATABASE: This property indicates the database name that will be created to store the catalog information. Default: opencga_catalog.
OPENCGA.CATALOG.DB.USER: This property should only be set if the MongoDB needs authentication. In this case, this property will contain the user name with permissions for the database. *This can be left empty in any case. The admin will be able to set this credentials using the command line.
OPENCGA.CATALOG.DB.PASSWORD: This property should only be set if the MongoDB needs authentication. In this case, this property will contain the password of the user with permissions for the database. *Like in the user property, this can be left empty. The admin will be able to set this credentials using the command line.
OPENCGA.INSTALLATION.DIR: This property is extremely important when using Tomcat to deploy the webservices. This property will have to point to the final OpenCGA installation directory after everything has been built. This property will be used by Tomcat to locate the configuration files. If this is not properly set, none of the webservices will work. Default: /opt/opencga.
OPENCGA.CATALOG.ROOTDIR: In Catalog, users are allowed to build their own directory structure, upload their own files, run analysis, etc. This path should be pointing to a physical location where Catalog will be storing those files and directory structure. By default, we normally put it in a folder called "sessions" within the installation directory (file:///opt/opencga/sessions/). Be aware of the "file://" annotation. In version 0.8 this is still necessary but will not be needed for future releases (see issue).
OPENCGA.STORAGE.VARIANT.DB.HOSTS:
OPENCGA.STORAGE.VARIANT.DB.USER:
OPENCGA.STORAGE.VARIANT.DB.PASSWORD:
OPENCGA.STORAGE.ALIGNMENT.DB.HOSTS:
OPENCGA.STORAGE.ALIGNMENT.DB.USER:
OPENCGA.STORAGE.ALIGNMENT.DB.PASSWORD:
OPENCGA.ANALYSIS.EXECUTION.MANAGER: OpenCGA Catalog allows users to run jobs. This property indicates how the jobs will be launched. At the moment we only support two types: LOCAL to run the jobs locally in a thread or SGE to run the jobs using Sun Grid Engine. More queuing systems will be supported soon.
OPENCGA.CLIENT.HOST: This property should be pointing to the URL where the webservices will be available. For development purposes, the default is http://localhost:8080/opencga/. This property is read by the command line opencga.sh in order to communicate with the webservices.
OPENCGA.CELLBASE.HOST:
OPENCGA.CELLBASE.VERSION:

You can copy this to ./m2/settings.xml:

Code Block

language	xml

    <profile>
     <id>localhost</id>
     <activation>
       <activeByDefault>true</activeByDefault>
     </activation>
     <properties>
       <CELLBASE.DB.MONGODB.HOST>localhost:9999</CELLBASE.DB.MONGODB.HOST>
       <CELLBASE.DB.USER></CELLBASE.DB.USER>
       <CELLBASE.DB.PASSWORD></CELLBASE.DB.PASSWORD>
       <CELLBASE.FILES.PATH>/home/imedina/data/cellbase/files</CELLBASE.FILES.PATH>

       <CELLBASE.DB.NEO4J.HOST>localhost:27017</CELLBASE.DB.NEO4J.HOST>

        <!--
       <CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE>admin</CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE>
       <CELLBASE.DB.MONGODB.READPREFERENCE>primary</CELLBASE.DB.MONGODB.READPREFERENCE>
        <CELLBASE.DB.MONGODB.READPREFERENCE>secondaryPreferred</CELLBASE.DB.MONGODB.READPREFERENCE>
        <CELLBASE.DB.MONGODB.REPLICASET></CELLBASE.DB.MONGODB.REPLICASET>
        -->
       <CELLBASE.REST.URL>http://bioinfodev.hpc.cam.ac.uk/cellbase/webservices/rest</CELLBASE.REST.URL>
       <CELLBASE.VERSION>v4</CELLBASE.VERSION>
       <CELLBASE.ENSEMBL.LIBS>/home/imedina/apis/ensembl/api_79</CELLBASE.ENSEMBL.LIBS>

       <OPENCGA.CATALOG.DB.HOSTS>localhost:27017</OPENCGA.CATALOG.DB.HOSTS>
       <OPENCGA.CATALOG.DB.PORT>27017</OPENCGA.CATALOG.DB.PORT>
       <OPENCGA.CATALOG.DB.DATABASE>opencga_catalog</OPENCGA.CATALOG.DB.DATABASE>
       <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.STORAGE.STUDY.METADATA.MANAGER></OPENCGA.STORAGE.STUDY.METADATA.MANAGER>

        <OPENCGA.CLIENT.HOST>http://bioinfodev.hpc.cam.ac.uk/opencga-1.0.0-rc3</OPENCGA.CLIENT.HOST>

        <OPENCGA.CATALOG.DB.TEST.DATABASE>catalogTest</OPENCGA.CATALOG.DB.TEST.DATABASE>
        <OPENCGA.CATALOG.TEST.ROOTDIR>file:/opt/opencga/catalogTest/</OPENCGA.CATALOG.TEST.ROOTDIR>

        <OPENCGA.CELLBASE.HOST>http://bioinfodev.hpc.cam.ac.uk/cellbase/webservices/rest/</OPENCGA.CELLBASE.HOST>
        <OPENCGA.CELLBASE.VERSION>latest</OPENCGA.CELLBASE.VERSION>

        <OPENCGA.STORAGE.VARIANT.DB.HOST>localhost:27017</OPENCGA.STORAGE.VARIANT.DB.HOST>
        <OPENCGA.STORAGE.VARIANT.DB.USER></OPENCGA.STORAGE.VARIANT.DB.USER>
        <OPENCGA.STORAGE.VARIANT.DB.PASSWORD></OPENCGA.STORAGE.VARIANT.DB.PASSWORD>
        <OPENCGA.STORAGE.VARIANT.DB.AUTHENTICATION_DATABASE></OPENCGA.STORAGE.VARIANT.DB.AUTHENTICATION_DATABASE>

        <OPENCGA.ANALYSIS.EXECUTION.MANAGER>LOCAL</OPENCGA.ANALYSIS.EXECUTION.MANAGER>

       <OPENCGA.CATALOG.ROOTDIR>/opt/opencga/sessions/</OPENCGA.CATALOG.ROOTDIR>

       <OPENCGA.INSTALLATION.DIR>/opt/opencga</OPENCGA.INSTALLATION.DIR>
     </properties>
   </profile>

After creating and configuring the default profile, you can build OpenCGA by executing the following command from the root of the cloned repository:

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