Documentation for JIRA 4.3. Documentation for other versions of JIRA is available too. 
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To move JIRA from one application server to another, for example from WebSphere to Tomcat, use one of the following methods:
Note
Regardless of which method you use, backup your data first and make sure you test JIRA on the new server before deploying it in production.
Follow the Upgrading JIRA instructions, installing the new version of JIRA on your new application server.
If you are using the same major version (e.g. 4.0.x) of JIRA on the old and new application server, you do not have to export your data. You can use your existing database with the new application server.
However, you cannot simply copy the WAR file or expanded WAR directory from an old JIRA EAR/WAR version in the old application server to the new application server. This will not work.
Follow these instructions:
UserTransaction as declared in the entityengine.xml file is correct for your server.