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I have a media computer running Ubuntu 12.04 and XBMC. I also have flexget and transmission-deamon set up to run automatically every hour with a line in my crontab.

@hourly /usr/local/bin/flexget --cron

Question is, I open XBMC on this machine by selecting 'XBMC' instead of 'Ubuntu' at the log in screen. Will my flexget and the transmission-daemon still run in the background?

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The transmission daemon will works exactly the same on Ubuntu and XBMC sessions.

I think you should not try to reconfigure the cronfiles, try rather to use config files or gtk interface.

Cordially,

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