[Bio-Linux] System on Parallels broken after updates

[Tauqeer Alam]

Thanks Tim! I understand your point. I will try to install one of them
myself.

Thank you again for all your help.

Tauqeer

On Wed, May 22, 2013 at 9:52 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> 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
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
> _______________________________________________
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>



-- 
*********************************************
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
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