Recently I installed Plex Media Server on my Ubuntu box. Here are what I did to make it run as my user so that it can index any of my media files without permission issues. The instructions here is for Ubuntu 14.04, but should be applicable to later Ubuntu version as well.
First, we need to tell Plex the user name it should run as.
In /etc/default/plexmediaserver, change the PLEX_MEDIA_SERVER_USER variable to the user name you want to run Plex as.
Second, we need to change the owner of Plex's App support directory. By default, it's /var/lib/plexmediaserver. If in doubt, you can check the PLEX_MEDIA_SERVER_APPLICATION_SUPPORT_DIR variable in /etc/systemd/system/plexmediaserver.service.
$ sudo chown -R user:user /var/lib/plexmediaserver
Finally, restart Plex server:
$ sudo service plexmediaserver stop $ sudo service plexmediaserver start
Now make sure that the server is running as the user you specified:
$ ps aux | grep "plex"