First, it would help if you would tell us a bit about the software you want to install.
Java gives you a few options.
You can keep all of your Java code on the server and let the users access it with a browser if you build your App with
Servlets and
JSP.
You could also deploy client side Java code as
applets or as a Java Web Start application which is a client side Java application that can be delivered via a browser, initially and then run as a local desktop application.
You'd have to tell us some more about what you're doing before anyone can suggest the best approach for you.