[BioPython] intalling on Windows, was: Re: can someone create biopython-1.42.win32-py2.5.exe

[Peter (BioPython List)]

Ann Loraine wrote:
> Hi,
> 
> Along these lines, a question:
> 
> I helped a student install biopython on his Windows laptop this week.
> However, we had a couple of problems getting BioPython to work
> properly with cygwin's python: our attempts to import Bio packages
> failed, I guess because they were not in cygwin's python's search
> path.
> 
> (We were able to get the cygwin's python to find a custom module he
> had written by setting PYTHONPATH properly, using Windows' Control
> Panel, and then checking python's search path in sys.path.)
> 
> How would I tell python where to find the BioPython packages? Is there
> a way to use PYTHONPATH environment variable to do this?
> 
> We will try this next time I meet with him, but any tips or advice you
> might have would be great.
> 
> Sorry for the possibly dumb questions -- I am not very familiar with
> how Windows does things.
> 
> Sincerely,
> 
> Ann Loraine

Hello Ann

Personally went I tried cygwin's python over a year ago, it did not seem 
very reliable (especially using idle).  Things my have improved but I 
would recommend you use the "pure windows" version of Python.

I suspect you are trying to combine cygwin's python with the 
pre-compiled windows setup.exe for BioPython.  This is probably not 
going to work - and having to mess about with PYTHONPATH would not 
surprise me.  The bits of BioPython written in pure python may be fine, 
but some of it is compiled C code... and then you asking for trouble.

Pure Windows (not using Cygwin)
===============================
For windows, I would recommend you to install a pure windows version of 
Python 2.5 and BioPython 1.42 using:

http://www.python.org/ftp/python/2.5/python-2.5.msi
http://biopython.org/DIST/biopython-1.42.win32-py2.5.exe

Or the Python 2.4 versions:

http://www.python.org/ftp/python/2.4.4/python-2.4.4c1.msi
http://biopython.org/DIST/biopython-1.42.win32-py2.4.exe

Or, if you have some good reason, the Python 2.3 versions.  Check the 
python website for the latest versions, these were correct at the time 
or writing.

It should "just work", without any messing about with paths.

Using cygwin on Windows (ignoring any pure windows python installation)
=======================
Basically follow the unix instructions.

Install the cygwin version of python, gcc, flex, ..., using cygwin setup.

Compile and install BioPython FROM SOURCE at the cygwin command line, 
using the cygwin version of python.

Peter