Any way to programmatically set boot device to usb?

I want to backup my boot drive to an image on a remote samba fileserver.

I am planning to set up a minimal ubuntu install on a usb flashdrive which would just take an image of the usual boot drive, then reboot back into the usual OS.

I would like to be able to leave the bootable usb plugged into the machine all the time as the machine is physically a bit difficult to get to.

Basically I want to be connected to the usual OS, and be able to issue a command which would shut down, then boot off the usb, which would image the drive onto the server, then reboot.

Is there a way to do this? Does anyone have any ideas how I can achieve this?

I want to make it as easy as possible to script backups of the boot drive without having to physically reinsert the usb drive every time.

Thanks!