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Installing and configuring OpenCGA consist of different steps, as you will see in this page you must first make sure that the server(s) have all dependencies installed, then you can configure and complete installation.

Installation and Configuration

Step 1 - Configuring the Server

OpenCGA requires Java 8, Tomcat or MongoDB. We try to keep dependencies to the minimum to ease development, installation and administration, and divide dependencies into required and optional. You can learn about all the dependencies and how to install them at Installation Guide > Server Configuration.

Step 2 - Getting OpenCGA

There are two main ways to get OpenCGA for installation:

  • You can download the source code from GitHub and use Apache Maven to compile and build it.
  • Or you can download a prebuilt binary from the OpenCGA GitHub Releases web page, notice that only stable and pre-releases are tagged and prebuilt.

Here you can learn more about these two options.

Building from Sources

Although most users will use stable prebuilt binaries (see below) there is still the need for different users to compile and build OpenCGA, for instance to test a development version. You can learn how to build from the source code at Installation Guide > Building from Source Code.

Download Binaries

You can download stable and pre-release (beta and release candidate) versions from OpenCGA GitHub Releases web page. You will find a tar.gz file with the name of opencga and the version, for instance to download OpenCGA 1.0.0-rc2.1 you can go to the GitHub Release at:

and download the file opencga-1.0.0-rc2.1.tar.gz from the Downloads section.

Step 3 - Install OpenCGA Binaries

These instructions assume that you have already downloaded or built openCGA binaries as described on Using Binaries and Building from Source Code.

Create an installation directory called /opt/opencga and copy the contents of opencga into this :

Note: In case of reinstallation, you must clean the installation directory (/opt/opencga)

mkdir /opt/opencga
cp -r build/* /opt/opencga

Step 4 - Configure OpenCGA

Execute the following command line to install and initialise Catalog database:

OpenCGA 2.0 Catalog Install
cd /opt/opencga
./bin/ catalog install <<< admin_P@ssword
OpenCGA 1.4.x Catalog Install
./ catalog install --secret-key any_string_you_want <<< admin_P@ssword

Step 5 - Deploy WAR file

This is main interface to perform any action with OpenCGA. User have two different options to start web services:

  • You can deploy OpenCGA in a Web Server.
  • Or you can use the OpenCGA admin command line.

Next you can learn more about these two options.

Deploying OpenCGA in a Web Server

Install Apache Tomcat and copy the deploy opencga.war. To do this, just copy it from the compilation directory (where you downloaded the OpenCGA repository) into the Tomcat webapps directory:

cp /opt/opencga/opencga.war $(path_to_tomcat)/webapps

path_to_tomcat is where you downloaded it, or probably /var/lib/tomcat8 if you installed via apt-get. Then, you should be able to see the swagger page at http://localhost:8080/opencga/. See Using RESTful web services for a tutorial.

Tomcat server will look for the configuration files in the installation directory, that can be changed in compilation time changing the property OPENCGA.INSTALLATION.DIR.

If the installation directory is empty at compilation time, the web services will search for the environment variable OPENCGA_HOME. If none of this is properly set, the webservices will not work.

Using the OpenCGA admin command line

The OpenCGA admin command line allows users to run embedded REST server. These webservices will be served with Jetty as follows:

/ server rest --start -p

Warning: This method is still under development.

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