USB-Blaster conflict with beaglebone serial debug cable

A trick? Perhaps - in the same way that you can have multiple USB-Blasters plugged into one machine and use them "at the same time" (as well as having other FTDI based hardware connected).

From the command prompt you can display the ID of all USB-Blaster cables with:

jtagconfig -n

You can then use the "-c" switch to specify a specific cable name when using the programmer from the command line:

quartus_pgm.exe -c "USB-Blaster " filename.cdf

You can do all this through the Quartus programmer GUI as well.

Hopefully this can get the Quartus side of things up. I'd hope there is an equivalent way to specify the Beaglebone serial cable to the relevant software.

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I don't ever see the USB-Blaster in Device Manager

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I've never known this. But if it's working I'd expect it to respond to the jtagconfig command above - which I'd trust.

Cheers,

Alex