This project currently hosts two tools (sub-projects): usb_jtag and nexys2prog.
Sources and more documentation for both can be found below and in the SVN repository, see the SourceForge project page for the latter.
Getting Help: Please read the documentation first, there is lots of it! If you still have questions, please go to to the support section of the project page, take a look if someone has already asked your question, and if not, use the support section to ask for help.
This firmware allows a USB-capable microcontroller - currently that's primarily the Cypress FX2 EZ-USB family, or an FTDI FT245 in combination with a CPLD - to act like an Altera USB-Blaster JTAG pod, which in turn may allow you to use tools you'd normally use with the Altera USB-Blaster, including available Linux tools such as UrJTAG.
This Perl script greatly simplifies the programming of a Digilent Nexys/Nexys2 board under Linux. It is well documented, see the links below.
A brief note on terminology: The term "FX2" can unfortunately refer to several things: The Cypress FX2 EZ-USB family, the KNJN (originally FPGA4FUN) Xylo, Saxo and other boards, or the Hirose FX2 connectors on the Digilent Nexys2 board, although I don't think the latter is talked about in the documentation. Here, we usually use FX2 to refer to the Cypress EZ-USB chips.