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You should check out the instrumentation forum here: https://forum.digilentinc.com/forum/8-scopes-instruments/

They should be able to help more with automating waveforms. If you can do what you are trying to accomplish with the scope attached to a Windows or Linux desktop, then it will just be a matter of porting your work to Linux on your embedded host.

This forum is for running embedded linux on FPGAs and Zynq devices.

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