How do I open Deja Dup as root?

1. Configure Deja Dup for your root backup: gksu deja-dup-preferences.

2. Run backup then with: gksu "deja-dup --backup".

At least this worked for me. (You have to configure Deja Dup for root, too, at first - next to your configuration for the "normal" user.)

As mythsmith says: "You can do that just for system folders, and still keep your home folder configured in your user account."

In 12.04 the following simple command works, if you have sudo privileges:

sudo deja-dup-preferences

Start by:

1. Run DEJA backup GUI and configure what you want to backup and where to save your backup files, without clicking backup now, just save your backup setting and exit Deja GUI.
2. Start terminal ALT+CTRL+T and type this command when you are ready to start backup sudo deja-dup --backup.

GUI window will open and backup should start.