What do you mean by " i don't know how to set url". What URL? Usually, the URL (or at least the hostname) used for a web application is assigned by the application server (Tomcat in your case) and should be of no consequence to your application.
And I think you are asking a general purpose packaging question. The answer depends heavily on what OS your customer is running. Windows customers might expect an installation program (MSI or EXE); InstallShiled can help you there. Linux customers might expect packages supported by their package manager. In either case I have at times provided a ZIP file with an
Ant script that performs the installation.
The other thing you have to consider is the licensing terms of the third-party software you are shipping. Tomcat should be OK, its Apache license is very lenient. But MySQL has a GPL license which places various burdens on you, the redistributor. Make sure you understand the licensing issues before you redistribute any open source software, they are not onerous but you want to make sure you are in compliance.