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

[Daniel Pass]

Ah, /usr/lib/pyshared/ only has python 2.6 on our BL6 machine, whereas
myself and the user who alerted me to it are using a local 2.7 installation
so that's why it's not finding it.

We're in the process of upgrading all the machines so I'll hold tight until
that's done.

Thanks Tim!
Dan


On 30 April 2013 14:03, Tim Booth <tbooth at ceh.ac.uk> wrote:

> 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
> _______________________________________________
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> Bio-Linux-dev at nebclists.nerc.ac.uk
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>



-- 



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
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