Numeric + Lapack/Blas/ATLAS [Re: [BioPython] Installation help]

[Michael Maibaum]

On 21 Dec 2004, at 14:09, Catherine Letondal wrote:

> Hi,
>
> On Dec 20, 2004, at 5:48 PM, Michael Maibaum wrote:
>
>> FWIW, there is a biopython package in DarwinPorts 
>> (http://darwinports.opendarwin.org/) which will automate this for 
>> you. (i.e. there is also a package for numeric.)
>>
>> Short story, you don't need to install extra stuff for Numeric, but 
>> there is a patch to make it build properly.
>
> Thanks for your help, it worked (it also re-installed another version 
> of Python...). I just had to change PYTHONPATH to contain /opt/local/ 
> directories (I want to stay with the python 2.4 I have just 
> installed), and to change setup.py to include /opt/local/include 
> directories. Is there a standard way to do that BTW ? - I mean without 
> changing setup.py?

Currently no, unfortunately. There are two problems, the first is 
co-operating with a python 'external' to DarwinPorts and the second is 
DarwinPorts current default for python2.3.

The first issue basically requires you to fiddle with PYTHONPATH, or 
just switch to using a  DarwinPorts provided python (e.g. python24).

I believe people are working on things so that it doesn't require 
python 2.3 (problem 2 above), and therefore would work with a python 
2.4 properly, In the mean time you could edit the darwinports code to 
prefer python 2.4 and things should 'just work'. To do that:

edit the python group code in 
'/opt/local/share/darwinports/resources/port1.0/group/python-1.0.tcl'

replace python23 with python24 and python2.3 with python2.4.

Once you've made that change, DarwinPorts should require python 2.4 for 
modules, and install modules in the correct place for that.

Hope that helps,


Michael


>
> Thanks in advance,
>
> --
> Catherine Letondal -- Institut Pasteur
> www.pasteur.fr/~letondal
>
>
>
-- 
Dr Michael Maibaum
Department of Biochemistry and Molecular Biology, UCL
email: maibaum at biochemistry.ucl.ac.uk