Installation

To run AnnotateGenomicRegions you need an installation of the Glassfish web server, which you can find here:

http://glassfish.java.net/

Follow the instructions to get Glassfish up and running on your computer. Then, download AnnotateGenomicRegions.war and deploy it. This can be done in at least three different ways:

1.Copy the AnnotateGenomicRegions.war file to the autodeploy folder of your Glassfish installation. For example, if you have your Glassfish installed on the C: drive as glassfishv3, this folder will be found at C:/glassfishv3/glassfish/domains/domain1/autodeploy
Glassfish will automatically deploy the application.

2.Deploy the AnnotateGenomicRegions.war file via the Glassfish administration web interface that is usually listening on port 4848 of your computer. (http://yourDomain:4848/ or http://localhost:4848/).

3.You might have Glassfish hooked up to an IDE such as NetBeans. Create a NetBeans project using the contents of the AnnotateGenomicRegions.war file and deploy from within NetBeans. Note that AnnotateGenomicRegions.war is essentially a zip file. Uncompress it to extract the content.

Please be aware that AnnotateGenomicRegions.war will deploy without problems on an Apache Tomcat server. However, the parameter parsing of the HttpRequest objects in AnnotateGenomicRegions uses Glassfish specific classes. Therefore, on Tomcat, the response you get will always be "no regions found to annotate".