<div dir="ltr"><div>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.<br></div><div>
<br></div><div style>We're in the process of upgrading all the machines so I'll hold tight until that's done.</div><div style><br></div><div style>Thanks Tim!</div><div style>Dan</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On 30 April 2013 14:03, Tim Booth <span dir="ltr"><<a href="mailto:tbooth@ceh.ac.uk" target="_blank">tbooth@ceh.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Dan,<br>
<br>
/usr/share/pyshared should not be directly in PYTHONPATH, but the<br>
package manager is supposed to symlink and byte-compile all the modules<br>
into /usr/lib/pymodules/python2.7. This is what I see on my system and<br>
so I can do this:<br>
<br>
===<br>
tbooth@balisaur[tbooth]python<br>
Python 2.7.3 (default, Aug 1 2012, 05:14:39)<br>
[GCC 4.6.3] on linux2<br>
Type "help", "copyright", "credits" or "license" for more information.<br>
>>> from Bio import SeqIO<br>
>>> import sys<br>
>>> print sys.path<br>
['', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2',<br>
'/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old',<br>
'/usr/lib/python2.7/lib-dynload',<br>
'/usr/local/lib/python2.7/dist-packages',<br>
'/usr/lib/python2.7/dist-packages',<br>
'/usr/lib/python2.7/dist-packages/PIL',<br>
'/usr/lib/python2.7/dist-packages/gst-0.10',<br>
'/usr/lib/python2.7/dist-packages/gtk-2.0',<br>
'/usr/lib/pymodules/python2.7',<br>
'/usr/lib/python2.7/dist-packages/ubuntu-sso-client',<br>
'/usr/lib/python2.7/dist-packages/ubuntuone-client',<br>
'/usr/lib/python2.7/dist-packages/ubuntuone-control-panel',<br>
'/usr/lib/python2.7/dist-packages/ubuntuone-couch',<br>
'/usr/lib/python2.7/dist-packages/ubuntuone-installer',<br>
'/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol',<br>
'/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode']<br>
>>><br>
tbooth@balisaur[tbooth]locate SeqIO<br>
/usr/lib/pymodules/python2.7/Bio/SeqIO<br>
<snip><br>
/usr/share/pyshared/Bio/SeqIO<br>
<snip><br>
===<br>
<br>
So it seems you have some issue with the Python package or with the<br>
Biopython package. What do you have in /usr/lib/pyshared/python2.7? I<br>
have 26 symlinks to .so files and 35 assorted directories. If you<br>
reinstall the packages does anything change, or do you get any useful<br>
error message?<br>
<br>
Cheers,<br>
<br>
TIM<br>
<div><div class="h5"><br>
<br>
<br>
On Tue, 2013-04-30 at 13:35 +0100, Daniel Pass wrote:<br>
> Hi All/Tim<br>
><br>
><br>
> Just been alerted by a user that biopython isn't on biolinux, although<br>
> of course it actually is.<br>
><br>
><br>
> I found that the default install is at /usr/share/pyshared/Bio/<br>
> (via dpkg -L python-biopython) but this isn't in the default<br>
> PYTHONPATH on either of our biolinux 6 or 7 machines hence the error.<br>
><br>
><br>
> I assume that this is a biolinux wide issue? And is there any advice<br>
> on adding the path for every user without manually exporting to<br>
> everyone's .bashrc?<br>
><br>
><br>
> Dan<br>
><br>
><br>
> --<br>
><br>
><br>
><br>
> Daniel Pass<br>
><br>
> Tel: (029208)76680<br>
> Mob: 07735658687<br>
> <a href="http://www.kille-morgan.org.uk" target="_blank">http://www.kille-morgan.org.uk</a><br>
><br>
> Room 0.39,<br>
> School of Biosciences,<br>
> Biological Sciences Building,<br>
> Museum Avenue,<br>
> Cardiff,<br>
> CF10 3AT<br>
><br>
<br>
</div></div>--<br>
Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
NERC Environmental Bioinformatics Centre<br>
<br>
Centre for Ecology and Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB<br>
<br>
<a href="http://nebc.nerc.ac.uk" target="_blank">http://nebc.nerc.ac.uk</a><br>
<a href="tel:%2B44%201491%2069%202705" value="+441491692705">+44 1491 69 2705</a><br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><br><br><br>Daniel Pass<br><br>Tel: (029208)76680<br>Mob: 07735658687<div><a href="http://www.kille-morgan.org.uk" target="_blank">http://www.kille-morgan.org.uk</a><br>
<br>Room 0.39,<br>School of Biosciences,<br>Biological Sciences Building,<br>Museum Avenue,<br>Cardiff,<br>CF10 3AT<br></div>
</div>