[Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)

[Tim Booth]

Hi Tony,

Great stuff - I didn't realise that apt-add-repository wasn't on there
by default and this has caused you various problems.  I'll modify the
script to sort that out and I think I can also easily fix the other
things you mentioned.

The nebc/bio-linux PPA should provide the version of Qiime necessary to
install bio-linux-qiime on Ubuntu 12.04.  There are a few helper
applications that the latest Qiime wants which are not yet packaged for
Bio-Linux, but the core features should all work.  What happens if you
try to install Qiime now that the PPA is added as a package source?

(here's how it should be)
tbooth at balisaur[tbooth]apt-cache policy qiime
qiime:
  Installed: 1.5.0+repack-2ubuntu4
  Candidate: 1.5.0+repack-2ubuntu4
  Version table:
 *** 1.5.0+repack-2ubuntu4 0
        500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ precise/main amd64 Packages
        100 /var/lib/dpkg/status
     1.4.0-0ubuntu2 0
        500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
     1.3.0-3 0
        500 http://gb.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
     1.3.0-0ubuntu6 0
        500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
     1.3.0-0ubuntu5 0
        500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
     1.2.1-ubuntu5 0
        500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages

Cheers,

TIM

On Thu, 2012-09-27 at 11:15 +0100, Tony Travis wrote:
> On 27/09/12 00:51, Tony Travis wrote:
> > On 26/09/12 18:56, Tony Travis wrote:
> >> [...]
> >> And I got:
> >>
> >> All done - your system is updated to Bio-Linux 7!
> 
> Hi, Tim.
> 
> I also had to install Ubuntu desktop to get NX working properly:
> 
>    aptitude install ubuntu-desktop
> 
> Then remove network manager, which should not be installed on a server:
> 
> > aptitude purge network-manager network-manager-gnome network-manager-pptp network-manager-pptp-gnome
> 
> Orphaned dependencies can be removed, and APT integrity checked by:
> 
> > aptitude -f install
> 
> Now I have all of Bio-Linux 7 accessible via NX except for Qiime.
> 
> Bye,
> 
>    Tony.
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> Bio-Linux-dev at nebclists.nerc.ac.uk
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-- 
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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