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I have an Ubuntu 12.04 Desktop machine running as a server with no input devices accessible after initial setup. I need to place any application that I want to run within the boot process. I have one application that I want to run that requires superuser access to run. Is there a way that I can automate that boot so I don't have to enter my password?

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Since Ubuntu uses Upstart, you need to write a custom job for Upstart:

Processes started during the boot sequence have superuser privileges, so you don't need to bother with sudo, passwords and stuff.

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