[Bio-linux-dev] biopython not in PYTHONPATH by default

[Tim Booth]

Hi Dan,

/usr/share/pyshared should not be directly in PYTHONPATH, but the
package manager is supposed to symlink and byte-compile all the modules
into /usr/lib/pymodules/python2.7.  This is what I see on my system and
so I can do this:

===
tbooth at balisaur[tbooth]python
Python 2.7.3 (default, Aug  1 2012, 05:14:39) 
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio import SeqIO
>>> import sys
>>> print sys.path
['', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2',
'/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old',
'/usr/lib/python2.7/lib-dynload',
'/usr/local/lib/python2.7/dist-packages',
'/usr/lib/python2.7/dist-packages',
'/usr/lib/python2.7/dist-packages/PIL',
'/usr/lib/python2.7/dist-packages/gst-0.10',
'/usr/lib/python2.7/dist-packages/gtk-2.0',
'/usr/lib/pymodules/python2.7',
'/usr/lib/python2.7/dist-packages/ubuntu-sso-client',
'/usr/lib/python2.7/dist-packages/ubuntuone-client',
'/usr/lib/python2.7/dist-packages/ubuntuone-control-panel',
'/usr/lib/python2.7/dist-packages/ubuntuone-couch',
'/usr/lib/python2.7/dist-packages/ubuntuone-installer',
'/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol',
'/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode']
>>> 
tbooth at balisaur[tbooth]locate SeqIO
/usr/lib/pymodules/python2.7/Bio/SeqIO
<snip>
/usr/share/pyshared/Bio/SeqIO
<snip>
===

So it seems you have some issue with the Python package or with the
Biopython package.  What do you have in /usr/lib/pyshared/python2.7?  I
have 26 symlinks to .so files and 35 assorted directories.  If you
reinstall the packages does anything change, or do you get any useful
error message?

Cheers,

TIM



On Tue, 2013-04-30 at 13:35 +0100, Daniel Pass wrote:
> Hi All/Tim
> 
> 
> Just been alerted by a user that biopython isn't on biolinux, although
> of course it actually is. 
> 
> 
> I found that the default install is at /usr/share/pyshared/Bio/
> (via dpkg -L python-biopython) but this isn't in the default
> PYTHONPATH on either of our biolinux 6 or 7 machines hence the error.
> 
> 
> I assume that this is a biolinux wide issue? And is there any advice
> on adding the path for every user without manually exporting to
> everyone's .bashrc?
> 
> 
> Dan
> 
> 
> -- 
> 
> 
> 
> Daniel Pass
> 
> Tel: (029208)76680
> Mob: 07735658687
> http://www.kille-morgan.org.uk
> 
> Room 0.39,
> School of Biosciences,
> Biological Sciences Building,
> Museum Avenue,
> Cardiff,
> CF10 3AT
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705