[Bio-linux-dev] issues installing qiime and denoiser

[Mattias de Hollander]

Hello Tim,

Regarding the Denoiser, I just found out the same at that issue is
solved.

With you hint the installation issue of matplotlib is also solved:

cloud at worker-5068:~$ apt-cache policy python-matplotlib
python-matplotlib:
  Installed: (none)
  Candidate: 0.99.3-1ubuntu4
  Version table:
     0.99.3-1ubuntu4 0
        500 http://us.archive.ubuntu.com/ubuntu/ natty/universe Packages
     0.99.1.2-3ubuntu1 0
        500 http://us.archive.ubuntu.com/ubuntu/ lucid/universe Packages
cloud at worker-5068:~$ apt-cache policy libgdk-pixbuf2.0-0
libgdk-pixbuf2.0-0:
  Installed: (none)
  Candidate: (none)
  Version table:

So now I see that the natty repositories have been mixed up on a lucid
system. Maybe that's because I used cloudbiolinux installation scripts.
If I disable these repositories everything installs fine.

Thanks!

Mattias




On Tue, 2011-09-20 at 17:15 +0100, Tim Booth wrote:
> Hi Mattias,
> 
> > I am trying to install Qiime and Denoiser on a fresh Ubuntu 10.04 LTS
> > installation, but I am running in some issues.
> > 
> > The bio-linux-denoiser package installs perfectly but conflicts with
> > bio-linux-qiime. 
> 
> This is because the latest Denoiser is built into Qiime, so you should
> simply remove bio-linux-denoiser and install only bio-linux-qiime.
> Sorry, I should have purged the obsolete package off the server.
> 
> > [145.100.30.212] out: The following packages have unmet dependencies:
> > [145.100.30.212] out:   bio-linux-qiime: Conflicts: bio-linux-denoiser
> > but 1:0.851-9 is to be installed
> > [145.100.30.212] out:   python-matplotlib: Depends: libgdk-pixbuf2.0-0
> > (>= 2.22.0) but it is not installable
> > [145.100.30.212] out: E: Broken packages
> 
> This is curious.  On my system python-matplotlib is a standard package
> (ie. supplied by Ubuntu servers) and does not have this dependency.
> Could you please send the output of "apt-cache policy
> python-matplotlib"?  I get this:
> 
> ===
> tbooth at barsukas[/tmp]apt-cache policy python-matplotlib
> python-matplotlib:
>   Installed: 0.99.1.2-3ubuntu1
>   Candidate: 0.99.1.2-3ubuntu1
>   Version table:
>  *** 0.99.1.2-3ubuntu1 0
>         500 http://gb.archive.ubuntu.com/ubuntu/ lucid/universe Packages
>         100 /var/lib/dpkg/status
> ===
> 
> > 
> > Regarding the Denoiser, are there any plans to upgrade the package to
> > the latest version (0.91). I am interested in that version because it
> > supports titanium reads. More info: http://www.microbio.me/denoiser/
> 
> The version of denoiser contained within the Qiime package definitely
> has the Titanium support included.  The website above states that the
> latest Denoiser will always be included in Qiime but if they change this
> policy then I'll split the packages out again.
> 
> Cheers,
> 
> TIM
> 
> -- 
> 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
> 


-- 
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands