[BioPython] installing biopython under cygwin

[Michiel Jan Laurens de Hoon]

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cl.exe is the Microsoft Visual C++ compiler. The fact that python is 
trying to run this compiler may indicate that the python you are running 
is the Windows' python instead of Cygwin's python. Try executing 'which 
python' on cygwin to see which python it is actually using. Also, make 
sure that the gcc compiler is installed on your cygwin. The gcc compiler 
should be the default for python under cygwin, normally you won't have 
to specify --compiler=cygwin.

The --compiler=mingw32 option is useful if you want to compile a python 
extension for Windows instead of cygwin. The resulting extension then 
does not rely on the cygwin1.dll shared library, but only on the 
standard Windows shared libraries. However, if you want to run python on 
cygwin, there is no need for the --compiler=mingw32 option.

--Michiel.


Brad Chapman wrote:

> Hi Daniel;
> 
> 
>>I'm trying to install the latest biopython in cvs
>>under cygwin. But the python setup.py build command
>>fails during the process when it tries to execute
>>"cl.exe" and cannot find that command. Is there a way
>>I can install biopython under cygwin?
>>
> 
> cl.exe is the Borland C++ compiler I believe. In the simplest case you
> should just need to specify:
> 
> python setup.py build --compiler=cygwin
> 
> or
> 
> python setup.py build --compiler=mingw32
> 
> (not sure what the difference is, but one might work :-) As you can
> probably tell, I haven't actually done this myself (only built with 
> Borland on Windows) but there is some info about it here:
> 
> http://www.python.org/doc/current/inst/non-ms-compilers.html
> 
> that might be helpful to you. Everything that works for distutils should
> work for biopython.
> 
> Hope this helps.
> Brad
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> 
> 
> 


-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon