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

[Tim Booth]

Hi Mike,

You shouldn't need to rename any files to make Qiime work, and if you do
rename any file owned by a package it will interfere with updates so
this is best avoided.  The path to the RDP classifier is set in the file
/usr/lib/qiime/shell/qiime_environment and it should be set
to /usr/share/rdp-classifier/rdp_classifier.jar unless you override it
with your own environment variable.  Nothing in the current Qiime
package refers to the version 2.2 jar explicitly.

I'm wondering if you had a similar problem before and you set
$RDP_CLASSIFIER manually but the setting you have is now wrong as I've
neatened things up a bit.  Can you please try doing "echo
$RDP_CLASSIFIER" both in a regular shell and at a QIIME shell prompt?
Then in a regular prompt try "env -u RDP_CLASSIFIER qiime" and again
"echo $RDP_CLASSIFIER" at the prompt.  That should reveal what is going
on.

Cheers,

TIM

On Wed, 2012-10-31 at 11:01 +0000, Michael Cox wrote:
> Hi Tim,
> 
> 
> I forgot to follow the below issue up with you whilst your were
> tackling the update - does the classifier need updating, or am I OK
> just to change the name of it?
> 
> 
> Thanks
> 
> 
> Mike
> 
> Begin forwarded message:
> 
> > From: "Cox, Michael J" <mikeyj.cox at gmail.com>
> > 
> > Subject: Re: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)
> > 
> > Date: 11 October 2012 15:02:44 BST
> > 
> > To: Bio-Linux technical discussion
> > <bio-linux-dev at nebclists.nerc.ac.uk>
> > 
> > 
> > Cheers Tim,
> > 
> > thanks for the tips.
> > 
> > Just been checking out QIIME - trying OTU picking to check
> > everything's still in place as we're retraining it with Silva - I'm
> > getting an error where it expects a .jar for the classifier to be
> > explicitly called version 2.2 (it's currently looking for it
> > in /usr/share/rdp-classifier.  I think we had this way back during
> > the initial QIIME installation.  
> > 
> > From the package lists I have both rdp-classifier 2.5+repack-3 and
> > bio-linux-rdp-classifier 2:1bl1-1 installed.  I'm guessing the
> > latter is the one that QIIME wants, can you confirm this is version
> > 2.2 and if so I'll edit the name.
> > 
> > Cheers
> > 
> > Mike
> > 


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