How to connect Spartan-6 with ISE 14.2 on Ubuntu
There is a set of Linux drivers by Michael Gernoth to replace the ones provided by Xilinx. I used them with a parallel cable, but they are designed for USB cables originally (though the Digilent USB cables are not in the list, but it might be worth a try).

I also needed to run ISE as root, and to preload the proper libraries. I did a writeup of my experiences, since there were also some other issues.