[Bio-Linux] Trinity added, Mothur and Mira updated

[Brian Cady]

Tim Booth, thank you for what you do,I use Bio-Linux daily, yet only use a small fraction of its capabilities.
Brian
 


     On Monday, September 14, 2015 6:42 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:
   

 Hi All,

I've been doing a round of package updates on Bio-Linux 8 over the last
week.  We now have both Mothur and Mira updated to the latest versions:

mira-assembler package is version 4.9.5
mothur package is version 1.36.1

Both will be updated by the package updater. If you experience any
problems or regressions with these new packages please let me know.

I'm also pleased to say that the Trinity RNA-Seq De novo assembler has
been added to the package repository (http://trinityrnaseq.github.io/).
Various modifications have been made to Trinity to make it integrate
nicely with the other packages on the system, so if you have problems
running it please let me know and I'll check if it is maybe something
that got messed up in the packaging.

trinityrnaseq package is version 2.0.6

To get it: sudo apt-get install trinityrnaseq
then just type: "Trinity" (with the capital T)

The credit for all this goes mainly to Michael and Andreas from the
Debian Med project who maintain these packages in Debian.  I've been
able to take what they made and backport it to Bio-Linux for you.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297


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