<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 TRANSITIONAL//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; CHARSET=UTF-8">
<META NAME="GENERATOR" CONTENT="GtkHTML/3.28.1">
</HEAD>
<BODY>
Hi,<BR>
<BR>
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.<BR>
<BR>
This is the list with versions that is available on my system:<BR>
<BR>
<PRE>
<FONT SIZE="2">qiime:</FONT>
<FONT SIZE="2"> Installed: (none)</FONT>
<FONT SIZE="2"> Candidate: 1.3.0-0ubuntu5</FONT>
<FONT SIZE="2"> Version table:</FONT>
<FONT SIZE="2"> 1.3.0-0ubuntu5 0</FONT>
<FONT SIZE="2"> 500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages</FONT>
<FONT SIZE="2"> 1.2.1-ubuntu5 0</FONT>
<FONT SIZE="2"> 500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages</FONT>
<FONT SIZE="2">bio-linux-qiime:</FONT>
<FONT SIZE="2"> Installed: (none)</FONT>
<FONT SIZE="2"> Candidate: 1:1.3.0bl-5</FONT>
<FONT SIZE="2"> Version table:</FONT>
<FONT SIZE="2"> 1:1.3.0bl-5 0</FONT>
<FONT SIZE="2"> 500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages</FONT>
<FONT SIZE="2"> bl1.1.0-9 0</FONT>
<FONT SIZE="2"> 500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages</FONT>
<FONT SIZE="2">python-cogent:</FONT>
<FONT SIZE="2"> Installed: (none)</FONT>
<FONT SIZE="2"> Candidate: 1.5.1-0ubuntu1</FONT>
<FONT SIZE="2"> Version table:</FONT>
<FONT SIZE="2"> 1.5.1-0ubuntu1 0</FONT>
<FONT SIZE="2"> 500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages</FONT>
<FONT SIZE="2"> 1.5-2 0</FONT>
<FONT SIZE="2"> 500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages</FONT>
<FONT SIZE="2"> 1.5-1 0</FONT>
<FONT SIZE="2"> 500 http://nl.archive.ubuntu.com/ubuntu/ natty/multiverse amd64 Packages</FONT>
<FONT SIZE="2"> 500 http://us.archive.ubuntu.com/ubuntu/ natty/multiverse amd64 Packages</FONT>
<FONT SIZE="2">bio-linux-python-cogent:</FONT>
<FONT SIZE="2"> Installed: (none)</FONT>
<FONT SIZE="2"> Candidate: 1:1.4.1bl-1</FONT>
<FONT SIZE="2"> Version table:</FONT>
<FONT SIZE="2"> 1:1.4.1bl-1 0</FONT>
<FONT SIZE="2"> 500 http://nebc.nox.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages</FONT>
<FONT SIZE="2"> 100 /var/lib/dpkg/status</FONT>
</PRE>
<BR>
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:<BR>
<BR>
<PRE>
<FONT SIZE="2">The following packages have unmet dependencies:</FONT>
<FONT SIZE="2"> python-cogent : Depends: python (< 2.7) but 2.7.1-0ubuntu5 is to be installed</FONT>
</PRE>
<BR>
Temporary disabling bio-linux repositories and installing python-cogent 1.5-1 from the main ubuntu repository gives this error while installing qiime:
<PRE>
<FONT SIZE="2">[194.171.8.5] out: The following packages have unmet dependencies:</FONT>
<FONT SIZE="2">[194.171.8.5] out: qiime : Depends: python-cogent (>= 1.5.1) but 1.5-1 is to be installed</FONT>
<FONT SIZE="2">[194.171.8.5] out: Recommends: cd-hit but it is not installable</FONT>
<FONT SIZE="2">[194.171.8.5] out: Recommends: rdp-classifier but it is not installable</FONT>
<FONT SIZE="2">[194.171.8.5] out: Recommends: fasttree but it is not installable</FONT>
</PRE>
<BR>
Did someone successfully install qiime using the bio-linux packages? Or can you suggest a solution?<BR>
<BR>
Any advice is appreciated.<BR>
<BR>
Thanks!<BR>
<BR>
<BR>
<TABLE CELLSPACING="0" CELLPADDING="0" WIDTH="100%">
<TR>
<TD>
<BR>
<PRE>
--
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
</PRE>
</TD>
</TR>
</TABLE>
</BODY>
</HTML>