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Lets say I open vlc or gimp on startup, but those commands don't return until the program closes. Does it just let a bash interpreter run indefinitely until they close or does it run and immediately kill the process unless I nohup or something? What's the appropriate way to startup these applications?

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Append an & to the program call in the shell script, and look into your desktop environment's preferred way to launch applications on login. – Daniel Beck May 24 '12 at 17:19

The .profile is read when bash starts. Starting another program from the shell does nothing to the .profile file.

Have a look at this: Difference between .bashrc and .bash_profile

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