[Bio-Linux] System on Parallels broken after updates

[Tim Booth]

Hi Tauqeer,

It would be nice to have some genome annotation tools on Bio-Linux but I
have to prioritise the needs of our supported NERC user community first.
If a pipeline is big and complicated to install, which these are, they
require correspondingly more effort to set up and maintain as packages
so I can't just add them as a quick job.  Their installation
instructions often ask you to set insecure configurations for the web
server or database servers which may be fine for individual users but I
can't apply these to every Bio-Linux installation.  There are also
licensing issues:

For MAKER, the pipeline itself is free but it depends on some components
(ie. TRF) that, according to the license, cannot be redistributed by
third parties.

Prokka also has the same problem.  Unfortunately the people who make the
tools that these "free" pipelines need explicitly don't want these
incorporating onto systems like Bio-Linux and apply licensing conditions
accordingly.

Cheers,

TIM

On Tue, 2013-05-21 at 19:08 +0100, Tauqeer Alam wrote:
> Hi Tim
> Thank you very much for being so helpful. I am from biology background
> so I do not understand too much details about the errors. Most of the
> time I try to solve by taking help from Google, but this one was kind
> of tricky.
> I would also like to take this opportunity to ask you
> another question. Do you have any plan to add genome annotation
> tools-such as AGeS (specially this one), Prokka, MAKER or BG7 in the
> BioLinux?
> 
> 
> Appreciate you help.
> 
> 
> Tauqeer
> 
> 
> 
> 
> On Tue, May 21, 2013 at 1:41 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:
>         Hi,
>         
>         Great to hear it was fixed so easily.  I do wonder why that
>         file might
>         have vanished in the first place.  Gremlins, I guess. ;-)
>         
>         Cheers,
>         
>         TIM
>         
>         
>         _______________________________________________
>         Bio-Linux mailing list
>         Bio-Linux at nebclists.nerc.ac.uk
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>         
> 
> 
> 
> 
> -- 
> *********************************************
> Md Tauqeer Alam, Ph.D
> Division of Infectious Diseases
> Emory University School of Medicine
> 615 Michael Street, Atlanta, GA 30322, USA
> tauqeer9 at gmail.com
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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OX10 8BB 

http://nebc.nerc.ac.uk
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