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Configuring the server
OpenCGA has some requirements such as requires Java, Tomcat or MongoDB. We try to keep dependencies to the minimum to ease development, installation and administration, we and divide dependencies into required and optional, you . You can learn about all the dependencies and how to install them at Installation Guide > Server Configuration.
There are two ways to get OpenCGA for the 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 hot how to build from the source code at Installation Guide > Building from Source Code.
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.
Install OpenCGA Binaries
Create an installation directory called /opt/opencga and copy the contents of opencga into this :
Note: In case of reinstallation, user you must clean the installation directory (/opt/opencga)
mkdir /opt/opencga cp -r build/* /opt/opencga
Setup Catalog Database
./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:
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
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 are is properly set, the webservices will not work.
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.
Standalone vs. Cluster
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