Altera's Quartus tools include some special software to download
bitstreams to their devices over USB (a DE-2 eval board, in my case).
They require some tricky work to set up properly on Fedora - my dev host
of choice. But you're in luck! I've packaged up an RPM that takes care
of this extra work for you. It creates a udev rule to set up the
USB-Blaster properly when you plug in your USB JTAG connection. It also
provides a service wrapper for Altera's jtagd daemon and moves some of
Altera's data files around so things just work. The sources are in
moxiedev, but I've posted the binary and source RPMs here for
convenience: http://moxielogic.org/tools/. Be sure to read the docs in
/usr/share/doc/moxie-quartus-altera-1 once installed. It assumes that
you've already installed Quartus II on your box (they don't package in
RPM format, unfortunately).
I'm told that the open source alternative UrJTAG may work for this device as well, but I haven't had a chance to look into it. Any experience worth sharing out there?