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

[Tim Booth]

Hi Anton,

I had a good look at the script and realised a couple of rogue spaces
had crept in at the end of two of the lines, which effectively made the
script buggy and caused these errors.  I'm surprised nobody else is
complaining, but in any case I've now fixed that problem.  How's it
looking at your end?

Cheers,

TIM


On Mon, 2012-12-03 at 09:27 +0000, GOSSNER Anton wrote:
> Hi Tim,
> 
> gossnera at gossnera-desktop[gossnera] dpkg -s python-biopython          [ 9:25AM]
> Package: python-biopython
> Status: install ok installed
> Priority: optional
> Section: python
> Installed-Size: 5835
> Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
> Architecture: amd64
> Version: 1.58-1
> Replaces: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
> Provides: python2.7-biopython
> Depends: python (<< 2.8), python (>= 2.7), python-support (>= 0.90.0), libc6 (>= 2.4), python-numpy, python-reportlab
> Recommends: python-biopython-doc (= 1.58-1)
> Suggests: python-tk, wise, muscle, clustalw, mafft, emboss, blast2
> Conflicts: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
> Description: Python library for bioinformatics
>  The Biopython Project is an international association
>  of developers of freely available Python tools for
>  computational molecular biology.
>  .
>  It is a distributed collaborative effort to develop Python
>  libraries and applications which address the needs of
>  current and future work in bioinformatics. The source code
>  is made available under the Biopython License, which is
>  extremely liberal and compatible with almost every license
>  in the world. We work along with the Open Bioinformatics
>  Foundation, who generously provide web and CVS space for
>  the project.
> Original-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
> Homepage: http://biopython.org
> Python-Version: 2.7
> gossnera at gossnera-desktop[gossnera]                                                                                     [ 9:25AM]
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> ________________________________________
> From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth [tbooth at ceh.ac.uk]
> Sent: 30 November 2012 17:13
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Upgrading to Bio-Linux 7 from 6
> 
> 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
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 

-- 
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