[Bio-Linux] Upgrading to Bio-Linux 7 from 6

[Tim Booth]

Hi Anton,

This is more likely a problem with my script than with your system, or
rather there is some minor issue and my script is making a meal of it.

What do you get when you ask dpkg specifically about biopython? - ie:

dpkg -s python-biopython

Also the thing with removing and reinstalling t-coffee is expected -
it's a crude workaround to a problem someone spotted during beta
testing.

Cheers,

TIM

On Fri, 2012-11-30 at 10:40 +0000, GOSSNER Anton wrote:
> Hi,
> 
> Just wondered if anybody is having the same problem and has solved it or if need to do a full install.
> 
> Following Tims instructions for upgrading, all gone well with initial upgrade of Ubuntu and start of Bio-Linux packages but always stops and exits with;
> 
> Verifying that everything installed...
> python-biopython  failed to install
> python-biopython-doc  failed to install
> Not all packages installed properly - exiting.
> 
> despite the fact python is installed;
> 
> Reading package lists... Done
> Building dependency tree       
> Reading state information... Done
> python-software-properties is already the newest version.
> 
> 
> Have removed and reinstalled via Synaptic Package Manager, restarted and rerun the script numerous times and various different combinations of installing and uninstalling  python but to no avail also run "apt-get autoremove"
> 
> No joy, any ideas?, also seems to uninstall Coffee and reinstall in every time I run the script.
> 
> Anton

-- 
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