[Bio-Linux] Latest Staden (Gap5) finally coming to BL, plus QIIME 1.7.0, and Acacia coming up

[Tim Booth]

Hi All,

I'm pleased to report that I have now uploaded packages for the latest
version of the Staden (gap5) trace and assembly editor to the package
repository.  The upgrade will not (yet) be installed by default but you
can get it immediately like so:

sudo apt-get remove bio-linux-staden
sudo apt-get install staden

Currently, this removes STARS and the assembly-conversion-tools, so
don't do this if you need these packages.
Subject to testing in the next couple of weeks, I'll then update the
bio-linux-staden package to make the new version the default.

There is also a new QIIME 1.7 release which I have packaged and this
will come through as an automatic update.  The package has passed all my
current tests but there are a few differences that may affect users,
especially if you have standard protocols or scripts.  See the release
notes here:

http://qiime.wordpress.com/2013/05/15/qiime-1-7-0-is-live/

I'll also add the Acacia denoising tool, which a lot of people like to
use with QIIME, to Bio-Linux, though as far as I can see the QIIME 1.7
release does not yet include a specific wrapper script for it.

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