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

[Cox, Michael J]

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

On 11 Oct 2012, at 14:31, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Mike
>> 
>> Internet restored.  Ran the update script and the package list script
>> and will forward both to you Tim, the list of things not installed is
>> quite long - includes galaxy, raxml and a number of r-cran packages.  
> 
> OK, something has definitely jammed then.  Hopefully the log will reveal
> the problem (looking at it now).  This also explains why NX didn't work
> at all, as the upgrade also does some things to try and fix this.
>> 
>> We can get around NX for the moment, I'll get people using putty or
>> winSCP in the meantime, but it's really helpful for a number of the
>> users that are used to desktop environments.  After sorting the
>> network connection, NX now working, but it seems much slower than it
>> was and various bits of the desktop are missing, sidebar the most
>> noticeable.  
> 
> The Unity desktop really depends on using the 3D capabilities of your
> graphics card and so is really not suitable for NX or remote X in
> general, hence you have to use the Gnome fallback as suggested by Tony,
> or else move to something like Xfce.  [ I'm not sure how
> hard/problematic this could be - not tried it on Ubuntu ].
> 
> One thing to bear in mind - and this is useful even if NX desktop is
> working perfectly - if that if a user can cope with the command line,
> they can set the NX Desktop option to "Custom", click "Settings", set
> Options to "Floating Window" and set Application to "gnome-terminal".
> Then instead of a full desktop, a terminal window will appear.  If you
> run a graphical application from that terminal then that will likewise
> appear.  This is faster than a full desktop.
>> 
>> Users definitely have ssh permissions as
>> per http://nebc.nerc.ac.uk/tools/bio-linux/accessing-bio-linux -
>> interesting list of stuff after recent NX login in auth.log one of
>> which seems to be related to a constant keychain message and the
>> screen-saver lock, which doesn't clear with entering the user's
>> password.  
>> 
> Not sure what to make of this.  You mean you have the screensaver
> running in the NX desktop window?  I'd just disable it.
> 
> More to follow off-list.
> 
> Cheers,
> 
> TIM
> 
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