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I'm running Kubuntu 12.04 and have a script written to log into my EC2 server. I would like to automatically have this run in the terminal just by clicking on it. Is this possible to do? I have tried making the default "open with" file the konsole with the run in terminal option selected, but that has not worked yet.

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Dolphin seems to have a bug where it sometimes doesn't respect your "open with" settings. –  Mechanical snail Aug 17 '12 at 5:59
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You can't really do this. You'll need to make a .desktop shortcut to it and then modify its properties to run in a terminal. Or you could convert the script to not require a terminal.

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