[Bio-Linux] new and updated packages for Bio-Linux

[Bela Tiwari]

Hello,

This is just an update about packages available for Bio-Linux:

1) bio-linux-blast has been udpated and contains  ncbi blast version 2.2.12.

2) bio-linux-emboss has been updated and contains version 3.0.0. 

This package checks if you have a file called /usr/local/bioinf/EMBOSS/EMBOSS/emboss/emboss.default. If you do, it will be saved during the installation and put back afterwards. Thus, any database specific information you have added should not be lost.
For those of you how have never looked at this file - you can specify remote and local database access methods and locations that allow users to access sequence (and related) files using EMBOSS programs such as seqret. The default version in the bio-linux-emboss package specifies embl, swissprot and trembl (aka uniprot) and refseq from the ebi. Genbank is also specified - from infobiogen in France. All are accessed using srs.

3) A new package called bio-linux-clcworkbench is available. This contains version 1.01 of the CLCFreeWorkBench from CLCbio. Information about this package is available here:

http://www.clcbio.com/index.php?area=software&section=free

At the moment, I would encourage you to try out this package before suggesting to all your users that they use it. It looks like it has great potential and we would be grateful for any feedback about it if anyone tries it out. Of particular interest is the fact that the people developing this intend it to be the base for an extended package that would be able to handle a wider range of sequence analysis tasks. 

After installation, the software can be started up by typing "clcwb" or "clcworkbench" on the command line.


The EMBOSS and blast packages will be updated automatically on your machines tonight (assuming you leave your  machine on and have not chosen to disable the automatic updating facility).

bio-linux-clcworkbench can be installed using synaptic. Information about installing packages using synaptic can be found here:

http://envgen.nox.ac.uk/envgen/software/archives/000503.html#Synaptic 


cheers

Bela 

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

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