I'm using a moates autoprom usb. The linux kernel (2.6.12) I'm running already had support for the autoprom's usb-serial converter (ftdi_sio) so this was a plug and play no-brainer. If you don't have it you'll need a FTDI FT232BM compatible driver and usbserial support. My system brought it up as /dev/tts/USB0, I'm running udev, those with devfs will probably see somehting like /dev/ttyUSB0 or you may have to make the node yourself. Check your kernel messages log, it should give you clues as to where the device node is. You'll need to check the permissions on the node to make sure the account you'll run tunerpro from can access it. Thats it on the hardware side.
Most distributions have a package available for it, if not you can download it from their home page http://www.winehq.com/. You can also find plenty of documentation on the emulator there. Once you have wine installed you can download and run the tunerpro instalation. Make sure you are logged in as the user you wish to run tunerpro as and run wine SetupTunerProRT_v400.exe. This will create your .wine directory (underwhich all your tunerpro files will be) and install tunerpro. You'll see the same setup wizard you're used to in windows.
Now there's just a bit more setup to do before you can start using tunerpro. First you have to setup a com port for wine so tunerpro can access your hardware. You'll need to create a symlink in your ~/.wine/dosdevices directory called com1 (or com2 or com3, it doesn't really matter) to your device. In my case my device was /dev/tts/USB0 so I would run the command:
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ln -s /dev/tts/USB0 ~/.wine/dosdevices/com1
Once thats all taken care of you should be able to start tunerpro
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wine ~/.wine/drive_c/Program\ Files/TunerPro\ RT\tunerpro.exe
So far I have run into two bugs both of which are mildly annoying but not enough to make me stop using tunerpro this way.
First off the emulation status window doesn't always get redrawn. Alot of times when you enable emulation it will still show not emulating even though it is. Doing something to force the window to be redrawn (minimize/restore, resize, etc) will make it change to the correct status.
It is also unable to verify the emulator ram with the current bin. It returns a fail -5 error. Some times it will log this error in the console: fixme:ntdll:FILE_AsyncReadService unexpected status 00000000. I'm assuming that tunerpro is making a call to a windows funciton that the emulator doesn't support.
I haven't tried aldl yet (due to an uncooperative car) but so far so good.