[Biopython-dev] [Bug 2815] Bio.Application command line interfaces

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2815





------- Comment #13 from biopython-bugzilla at maubp.freeserve.co.uk  2009-04-28 12:39 EST -------
(In reply to comment #11)
> In those unittests, you'll note that I have no idea about the windows
> environment! (dont use window, never have used windows). I just copied
> from the Emboss wrapper...
> 
> C.

That explains things :)

I had already guessed you hadn't run any of these tests on Windows, because the
executable isn't recorded properly, and even if it was, you never use it when
creating the command line objects:

#Don't do this if you want to actually run the application, as
#it would only work on Unix where the command is on the path:
#cmdline = MafftCommandline()
#Instead, use the exe name we determined earlier:
cmdline = MafftCommandline(mafft_exe)

The EMBOSS installer is nice and *does* setup EMBOSS_ROOT, which is why
test_Emboss.py looks for it.

However, for test_Clustalw_tool.py I just made a list of the default install
locations, and check them.  There is no environment variable!

I haven't looked at the documentation but I would be pleasantly surprised if a
MAFFT_ROOT environment variable was setup by the default method of installing
MAFFT on Windows (and similarly for the other tools).

If the tools do record their install location in the registry, we can do a
win32api call to get the path.  Then if win32api isn't installed just raise the
MissingExternalDependencyError exception.

If you look at my test_Muscle_tool.py in CVS, you'll see I haven't yet
determined how best to try and locate MUSCLE. 

Peter


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