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Finally log out and log back in. You should now see the tomcat icon on the system tray.
Setup Tomcat B
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To set up another instance of Tomcat, I would call it tomcat-b, simply copy the tomcat-a directory, change the ports as outlined in Ubuntu 5.0 Portable Tomcat 6.x & Instances and repeat Automatic Startup and Shutdown of Tomcat and Tomcat Icon on System Try Tray with adjustment for the different name and directory.
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