[Bio-Linux] Updated QIIME package 1.8.0

[Bramwell, Jason]

Tim,
What do I have to do to get these (and other) updates? The documentation
is saying that updates should occur every night but this does not seem
to be the case for me (689 packaged required yesterday and 689 packages
still required today). So far I've been running apt-get update/upgrade
but is this the correct way or is there a 'bio-linux' way of doing this?

So far when I update a fresh install there are 689 update packages which
I can install but then FastTree, Glimmer, Galaxy, Mira and QIIME are
held back. Am I doing this correctly or should i be following an
alternate method?

Thanks
Jason Bramwell

-----Original Message-----
From: Tim Booth [mailto:tbooth at ceh.ac.uk] 
Sent: 10 March 2014 14:24
To: Bio-Linux mailing list
Subject: [Bio-Linux] Updated QIIME package 1.8.0

Dear Bio-Linux users,

I've packaged the latest QIIME 1.8.0 which came out late last year.  The
package will appear in available updates later today.  Please be aware
that this has some differences from the previous release, particularly
that it uses Emperor by default rather than KiNG for 3D plots (though
the latter can still be used).  You may need to modify your procedures
or scripts.  The QIIME tutorial in the introductory course notes is
still being updated to reflect the changes.

I have also now included the Greengenes core set and lanemask files
within the qiime-data package as these have not changed in months and
they are now included as standard with other QIIME releases.

I still can't include USearch or Rtax due to copyright restrictions, and
I've not bothered packaging pplacer or sourcetracker yet but if anyone
is really keen to get these included please let me know.

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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