The FPGA is not programmed through a JTag, but through some "homemade" USB connection. Avnet has made a tool called AvProg for this connection, which is Windows only (shame on them!) :(

It is, however, fairly easy to get working under Linux using Wine.

Start by downloading AvProg from avnet.com, which requires you to register.

Next unzip the archive and install it into Wine

mkdir AvProg
cd AvProg
unzip AvProg_v340i.1_setup.zip
wine setup.exe
cd ..
rm AvProg -r

When the eval board is connected it will be attached to /dev/ttyACM0 (or another number). This device has to be made to comx inside Wine. This is done like this

cd ~/.wine/dosdevice
ln -s /dev/ttyACM0 com1

Removing the Skins directory will disable the fancy coloured GUI and make the application much better under wine (explanation):

cd ~/.wine/drive_c/Program\ Files/Avnet/AvProg/
rm -rdf Skins

That's it, write some VHDL/Verilog, make a bit file and run AvProg

wine ~/.wine/drive_c/Program\ Files/Avnet/AvProg/AvProg.exe

and have fun :)