Preparation

Configuring the server

OpenCGA requires Java, 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.

Getting OpenCGA

There are two ways to get OpenCGA for installation. First, you can download the source code from GitHub and use Apache Maven to compile and build it. Second, you can download a prebuilt binary from the OpenCGA GitHub Releases web page, notice that only stable and pre-releases are tagged and prebuilt.

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:

https://github.com/opencb/opencga/releases/tag/v1.0.0-rc2.1

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

Installation

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

Configure OpenCGA

Setup Catalog Database

./opencga-admin.sh catalog install --secret-key any_string_you_want <<< admin_P@ssword

./opencga-admin.sh catalog install --algorithm HS256 --secret-key any_string_you_want -p <<< admin_P@ssword

Deploy WAR file

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

1. 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.

1. Serving the webservices using the admin command line. These webservices will be served with Jetty as follows:

   /opencga-admin.sh server rest --start -p

Warning: This method is still under development.

Other considerations

Hardware specifications

Standalone vs. Cluster