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This is a question that involves multiple issues involved in creating a menu tied to a Launcher icon. I'm using a fresh install of 12.04 (AMD64 version).

I've written a small yad (Yet Another Dialog editor) script which displays a dialog containing several choices for launching a set of related programs.
Some are applications installed normally using the Ubuntu Software center and some are java programs called by commands of the form java -jar JARFILENAME.jar. If I launch an application by clicking on a desktop file in /usr/share/applications it launches and puts an icon in the Launcher until I close the application.
The same happens if I run them from the command line in a terminal. However if I call them using an exec command in the script they launch by there is no new icon in the launcher.

They run fine, but if I have more than one open on different desktops it would be nice to have the icons in the launcher to switch focus rather than having to use the Workplace Switcher.

Now about the java apps--I'd like them to also have icons on the Launcher when they're running. Running them by clicking on an APPNAME.desktop file with the icon specified works, but what is the correct syntax for running them with the bash script exec command?

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You probably will want to directly call the launchers from the script, And create custom launchers for the java programs, Running a .desktop file in the terminal

How to make a launcher(.desktop file) for a binary file?

How can I add a bash script to the Unity launcher?

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