I just had to do something similar, because I switched to a mac book pro. I finally got ATR working with Virtual Box and Windows 7. It takes some work and configuration. You kinda need to know what you're doing, or follow some guide (there's probably one in MSF if you need instructions), because this stuff isn't exactly intuitive. It's kinda silly to have a windows VM just to run ATR, but oh well. Anyway, you should be able to do the same in a Ubuntu host, since Virtual Box works in Ubuntu. AP manager should work as well, as long as you set up USB correctly on Virtual Box (so that your VM has access to your AP when you plug it in).
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