I haven't tried getting Apertium to run natively on Windows (didn't
want to deal with that headache xD), but I do have it running inside
Cygwin.
The easiest way to get it running is to dump it inside your Cygwin
home directory (which would typically be <Cygwin path>\home\<Cygwin
username>) and run it from there inside the Cygwin environment (the
Cygwin bash shell). The Cygwin username is typically the same as your
Windows username.

If you want, you could also brave mounting the existing location as a
folder inside your Cygwin environment (see
http://www.cygwin.com/cygwin-ug-net/using.html#using-pathnames ) for
more information about that. However, I think just moving the folder
would be easier.

A third option is to access it via the /cygdrive/ mount, which allows
you to access your entire Windows filesystem through it. However, I
ran into some issues when trying to access the files that way, IIRC. I
don't remember exactly what they were, but I do seem to remember that
they had to do with how the /cygdrive/ mount is defined and handled,
and that's why I ended up mounting my Apertium folder into a folder
under my home directory.

I just did a sparse checkout from SVN, and then compiled from source
in the Cygwin environment. Following these instructions worked pretty
well for me: 
http://wiki.apertium.org/wiki/Apertium_on_Windows#Building_under_Cygwin

Hope this helps! ^^

-- Stephen

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