[Bio-linux-dev] Confusing and conflicting versions of Qiime on Ubuntu 11.04

[Mattias de Hollander]

Hi,

After a successful installation of the qiime bio-linux package on a
lucid 10.04 LTS system I am trying it on a recent 11.04 natty
installation. I am running  in some problems and I am a bit confused
about the different qiime and python-cogent packages in the repository.

This is the list with versions that is available on my system:


qiime:
  Installed: (none)
  Candidate: 1.3.0-0ubuntu5
  Version table:
     1.3.0-0ubuntu5 0
        500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
     1.2.1-ubuntu5 0
        500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages


bio-linux-qiime:
  Installed: (none)
  Candidate: 1:1.3.0bl-5
  Version table:
     1:1.3.0bl-5 0
        500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
     bl1.1.0-9 0
        500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages



python-cogent:
  Installed: (none)
  Candidate: 1.5.1-0ubuntu1
  Version table:
     1.5.1-0ubuntu1 0
        500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
     1.5-2 0
        500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
     1.5-1 0
        500 http://nl.archive.ubuntu.com/ubuntu/ natty/multiverse amd64 Packages
        500 http://us.archive.ubuntu.com/ubuntu/ natty/multiverse amd64 Packages

bio-linux-python-cogent:
  Installed: (none)
  Candidate: 1:1.4.1bl-1
  Version table:
     1:1.4.1bl-1 0
        500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
        100 /var/lib/dpkg/status


Installing the normal way using apt-get install bio-linux-qiime qiime
python-cogent selects python-cogent from the bio-linux repository, but
this package depends on python 2.6 or lower. Unfortunately python 2.7 is
the default on natty, giving this error:


The following packages have unmet dependencies:
 python-cogent : Depends: python (< 2.7) but 2.7.1-0ubuntu5 is to be installed


Temporary disabling bio-linux repositories and installing python-cogent
1.5-1 from the main ubuntu repository gives this error while installing
qiime:

[194.171.8.5] out: The following packages have unmet dependencies:
[194.171.8.5] out:  qiime : Depends: python-cogent (>= 1.5.1) but 1.5-1 is to be installed
[194.171.8.5] out:          Recommends: cd-hit but it is not installable
[194.171.8.5] out:          Recommends: rdp-classifier but it is not installable
[194.171.8.5] out:          Recommends: fasttree but it is not installable


Did someone successfully install qiime using the bio-linux packages? Or
can you suggest a solution?

Any advice is appreciated.

Thanks!




-- 
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20110921/0402b062/attachment.html>