GERMS in NIOS2?

If you want the germs just to be able to download code, then you have an easier solution.

The IDE they give you is capable of downloading code to the NIOS II (you have to include at least the minimal debug module).

Basically I just created a really big RAM and downloaded my compiled code into it. I'm assuming you have to also have the JTAG UART core

included as well (don't quote me on that thought, i just put it in anyway because I figured the debug module needs it there too).

In the software tutorial on the Altera site they give an example of doing this.