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Question: is it necessary to start a NIOS IDE shell first? Can we just run quartus_stp -s from the Windows/DOS command prompt and go from there?
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The NIOS IDE shell is pretty much identical to a Windows/DOS command prompt. Did you try and bring one up?
quartus_stp should work for both, however, the paths to the Altera tools might not be setup correctly. The advantage of using the Altera bash shell is that the paths are all correct.
I have several versions of Quartus installed, and Cygwin, and I find it much less trouble if I just use the shell from the specific Altera installation.
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We're trying it currently without anything to do with NIOS
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The NIOS II IDE Shell is just what its called on the Windows Start Menu. It doesn't have to involve a NIOS processor in your design.
Cheers,
Dave