On-Premise HPC Cluster
You can install OpenCGA on a local HPC cluster. Installing and configuring OpenCGA consists of different steps, as you will see on this page you must first make sure that the server(s) have all dependencies installed, then you can configure and complete the 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 binaries from OpenCGA GitHub Releases, notice that only stable and pre-releases are tagged and built, if you want to test a development version see next point.
Or You can download the source code from GitHub and use Apache Maven to compile and build it.
Please visit Getting OpenCGA to learn more about these two options.
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)
Step 4 - Configure OpenCGA
Execute the following command line to install and initialise Catalog database:
Step 5 - Deploy WAR file
This is the main interface to perform any action with OpenCGA. User has 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, which 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 web services will not work.
Using the OpenCGA admin command line
The OpenCGA admin command line allows users to run an embedded REST server. These web services will be served with Jetty as follows:
/opencga-admin.sh server rest --start -p
Warning: This method is still under development.
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