Hi, TJF! Thanks for your reply, I wasn't aware of such a lib. Will 
definitely look into it.
As for my issue, after a whole day trying, I  found out that there were 
major differences between 3.8 and 4.0+ kernel versions regarding how it 
deals with device tree overlays and addressing of GPIO. I was mixing dts 
files for the newer kernel and the older kernel. I manage to get it fully 
working by making a clean install of machinekit, as described 
in https://machinekoder.com/machinekit-debian-stretch-beaglebone-black/ .
Thanks for your input!

Best Regards.
Paulo Sherring.

Em quarta-feira, 26 de setembro de 2018 11:42:16 UTC-3, TJF escreveu:
>
> Hi Paolo!
>
> You could use libpruio <https://github.com/dtjf/libpruio> for pinmuxing. 
> It also provides QEP features (A freq only, AB speed and position, as well 
> as ABI impulse synced speed and position). Find installation instructions 
> in the on-line documentation 
> <http://users.freebasic-portal.de/tjf/Projekte/libpruio/doc/html/ChaPreparation.html>
> .
>
> Best regards.
>
> Am Dienstag, 25. September 2018 23:25:32 UTC+2 schrieb Paulo Sherring:
>
>> Hi, everybody!
>> I am having trouble trying to use machinekit, config-pin and a non 
>> default pinmux state.
>> What I want to do is to configure P9_27 and P9_92 to be used by the 
>> quadrature encoder peripheral and leave P9_25 alone.
>> If I use config-pin to configure it to qep, it disables by default pull 
>> up, which I need, since I didn't include it in my custom PCB.
>> If I use a custom device tree to setup QEP, all pins are claimed and I 
>> cant use P9_25 throgh machinekit, as IO.
>> I guess I could use a memdev like program to enable it by hand. I did it 
>> in the past, but, I feel that it is the cheaters way to do it.
>> I never really understood device tree, it was always trial and error or 
>> raw memory RW with me :/
>>
>> In help is very welcome.
>> Thanks in advance.
>> Paulo Sherring.
>>
>

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