@slacker, I think what @murthy425 was referring to was the procedure to get the USB Blaster and Ubuntu 9.04 working as cited in this post.
http://www.alteraforum.com/forum/showthread.php?t=5893 I read this post a couple weeks back when I was still using 9.04 and it seemed to work at the time.
Now, I'm not sure what I have going on, but I am running on 9.10. (I knew it was a bad idea.)
It seems like the thing works, but once in a while I have to run this script:
sudo killall jtagd
sudo /home/dave/altera9.0/quartus/bin/jtagconfig -n
because I get an error code 89.
or something like this:
There is a problem with the Quartus II installation on your computer.
Please use `jtagconfig` for further diagnosis.
Overall, the installation of quartus on Ubuntu was a little rough, but it seems to be working on my 32-bit 9.10. I still get a seg fault on the AMD64 version of 9.04.
Altera, please support Ubuntu! All the cool kids are using it ;)
Dave ...