You should let your initscript fix this issue. I have one like https://gist.github.com/MendelGusmao/5398362 which starts a btsync process for each user in a given list and uses ~/.sync/config.json . There are many ways for root to start a process as a user, initscrips fpr debian usually use start-stop-daemon. "apt-get only works as root" is (almost)true on the one hand but utterly unrelated. Even if you don't use any initscript at all you can simply run the "apt-get installed" program as user. Take care, "@reboot" is not supported by all cron daemons, check your local manpage.