Your best option is to use Wine and install PiPP and Autostackert. The Windows programs run fine under Wine.
For Capture I suggest using Planetary Imager: blog.gulinux.net/en/planetary-imager
That works better for me than Ekos video capture.
Camera was an ASI1600MC-Cool. I used Planetary Imager (native) on a Zotac pi332 running Ubuntu Mate 16.04 (not Windows).
I processed the .ser file (50fps, ~8000frames total) directly in Autostackert running under Wine on a Desktop running Ubuntu 16.04. Note that this is memory intensive, so you can't expect to do that on a Pi3!
The low quality results from Jupiter being very low (20 deg above horizon with lots of turbulence) by the time I dragged myself out of bed this morning, and the fact that the focal length of my telescope was only 1600 mm (8" Ritchey, no Barlow or extender used). Jupiter itself covered barely 70 or 80 px on my sensor, so I couldn't expect more (this image is 3x Drizzled).
Anyway, this is just to demonstrate that you can capture and process planetary images on Linux without having to resort to a Windows machine.
I assume that was your question.
Last edit: 5 years 11 months ago by Jose Corazon. Reason: Add more info
Yes, that's exactly what I want to do. My main processing machine with PixInsight is Linux only, so I want to build up the tools there for solar and planetary.