Hi guys,
I am starting to think we should not include Cygwin as a target  
platform, but instead only regular Windows.  The problem is that the  
Cygwin version of Python thinks it's operating in a unix path  
environment, but as soon as it sends path arguments to a Windows  
program (like the NCBI blast executables for Windows), the Windows  
program will barf on those unix style paths.  The basic difficulty is  
that in a Cygwin environment, there is a mix of native-Windows  
programs and cygwin programs, so paths that work for the latter will  
not work for the former, and as far as I know there is no easy,  
systematic way to insulate yourself from this madness...

- do we need to support Cygwin?  Or can we just support native  
Windows?  As I understand it, the main advantage of Cygwin is for open  
source developers who want to compile / re-compile C extensions (i.e.  
cygwin includes the free mingw compiler; in native Windows you would  
need to buy the Visual Studio 2003 compiler package).

- is there a simple solution I am missing?

-- Chris


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