[BioPython] Windows Install Question

[Andreas Matern]

Brad,

You are a god.   I used the Borland C++ compiler, as it's FREE, and used
both your page (@bioinformatics.org) and Gordon William's page to get it
going.

Only modifications were that I'm using Active State's ActivePython2.1 so
I needed to make slight name changes.

And, of course, I had to set my PYTHONPATH to my biopython install
directory....

The only failure that the setup.py test package gave me was
Failure:test_SubsMat

interestingly, the Assertion Error is:

Output : 'M 0.00 0.40 0.70 0.80 1.00\n'
Expected: 'M -0.00 0.40 0.70 0.80 1.00\n'

Wonder why the - sign?

In any event, I'll start playing with BioPython using ActivePython 2.1
on WinNT, and let y'all know when I run into a brick wall...

-Andreas

P.S. As for maintaining the Windows installers . . . . um, give me some
time, eh? 



Brad Chapman wrote:
> 
> Hi Andreas, Jeff;
> 
> Andreas:
> > > >error: command 'cl.exe' failed: No such file or directory
> 
> Jeff:
> > > I've not used Biopython on windows before, but it looks like it's
> > > expecting a compiler called "cl.exe" and not finding it.
> 
> Yup, right on target. It's set up to use the microsoft c++ compiler
> by default.
> 
> Andreas:
> > I have a C++ compiler installed, but I don't know how to specify that
> > for Distutils.
> 
> If you have Borland C++ installed, I have written up instructions in
> the Tutorial for setting it up and compiling with it:
> 
> http://www.bioinformatics.org/bradstuff/bp/tut/Tutorial.html
> 
> See section 1.3.2. I'm no windows expert, by far, but I use this to
> compile the installers (which you could also use to prevent having
> to compile it, if you don't want to mess around with the compilers).
> 
> Andreas:
> > If you'd like, once this works, I can write up what I've done to get
> > biopython working for windows...
> 
> If you have a different C++ compiler and have time to write up
> instructions that would be super. Changes, suggestions for the
> current docs are also very welcome. You can check out the distutils
> documentation at:
> 
> http://www.python.org/sigs/distutils-sig/doc/
> 
> to see if your compiler is supported by distutils.
> 
> > > >How does one change python's search path?  I installed python on a UNIX
> > > >box, changing the --prefix to a writeable area.
> 
> You can set the PYTHONPATH environmental variable to point to
> directories python should look in for libraries. It is a normal
> colon separated unix variable:
> 
> /first/directory/with/python/files:/second/directory/with/python/files
> 
> I think it is similar on windows, but I'm not familiar enough with
> windows to know the exact syntax.
> 
> > > >Thanks for your help, looking forward to contributing/working with
> > > >biopython...
> 
> Well, if you'd like to maintain the windows installers, I'd love
> that :-). There is always plenty to do around here!
> 
> Brad
> --
> PGP public key available from http://pgp.mit.edu/

-- 


------------------
Andreas Matern
Bioinformatician
LION Bioscience Research, Inc.
141 Portland Street, 10th Floor
Cambridge, MA 02139

andreas.matern@lbri.lionbioscience.com
phone: (617) 245-5483
fax:   (617) 245-5499