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

[Tim Booth]

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

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