Hi,
The ISE Webpack license is sufficient to compile the FPGA firmware "fpga.bin".
FPGA can be programmed via the JTAG port (in-circuit) without special setup, but it is simpler to use the oscilloscope software and program it via USB. When you run the software and connect to hardware, the software first searches for a FX2 device and uploads the firmware image "fx2.hex" to FX2 internal RAM. After the upload, the FX2 device is reset and configured (the process is called re-numeration), and the file "fpga.bin" is sent to FX2 to program the FPGA.
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Regards,
Dejan