<div dir="ltr">Thanks Tim! I understand your point. I will try to install one of them myself.<div><br></div><div>Thank you again for all your help.</div><div><br></div><div>Tauqeer<br><br><div class="gmail_quote">On Wed, May 22, 2013 at 9:52 AM, Tim Booth <span dir="ltr"><<a href="mailto:tbooth@ceh.ac.uk" target="_blank">tbooth@ceh.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Tauqeer,<br>
<br>
It would be nice to have some genome annotation tools on Bio-Linux but I<br>
have to prioritise the needs of our supported NERC user community first.<br>
If a pipeline is big and complicated to install, which these are, they<br>
require correspondingly more effort to set up and maintain as packages<br>
so I can't just add them as a quick job. Their installation<br>
instructions often ask you to set insecure configurations for the web<br>
server or database servers which may be fine for individual users but I<br>
can't apply these to every Bio-Linux installation. There are also<br>
licensing issues:<br>
<br>
For MAKER, the pipeline itself is free but it depends on some components<br>
(ie. TRF) that, according to the license, cannot be redistributed by<br>
third parties.<br>
<br>
Prokka also has the same problem. Unfortunately the people who make the<br>
tools that these "free" pipelines need explicitly don't want these<br>
incorporating onto systems like Bio-Linux and apply licensing conditions<br>
accordingly.<br>
<br>
Cheers,<br>
<br>
TIM<br>
<div class="HOEnZb"><div class="h5"><br>
On Tue, 2013-05-21 at 19:08 +0100, Tauqeer Alam wrote:<br>
> Hi Tim<br>
> Thank you very much for being so helpful. I am from biology background<br>
> so I do not understand too much details about the errors. Most of the<br>
> time I try to solve by taking help from Google, but this one was kind<br>
> of tricky.<br>
> I would also like to take this opportunity to ask you<br>
> another question. Do you have any plan to add genome annotation<br>
> tools-such as AGeS (specially this one), Prokka, MAKER or BG7 in the<br>
> BioLinux?<br>
><br>
><br>
> Appreciate you help.<br>
><br>
><br>
> Tauqeer<br>
><br>
><br>
><br>
><br>
> On Tue, May 21, 2013 at 1:41 PM, Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>> wrote:<br>
> Hi,<br>
><br>
> Great to hear it was fixed so easily. I do wonder why that<br>
> file might<br>
> have vanished in the first place. Gremlins, I guess. ;-)<br>
><br>
> Cheers,<br>
><br>
> TIM<br>
><br>
><br>
> _______________________________________________<br>
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><br>
><br>
><br>
><br>
><br>
> --<br>
> *********************************************<br>
> Md Tauqeer Alam, Ph.D<br>
> Division of Infectious Diseases<br>
> Emory University School of Medicine<br>
> 615 Michael Street, Atlanta, GA 30322, USA<br>
> <a href="mailto:tauqeer9@gmail.com">tauqeer9@gmail.com</a><br>
><br>
<br>
</div></div><div class="im HOEnZb">--<br>
Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
NERC Environmental Bioinformatics Centre<br>
<br>
Centre for Ecology and Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB<br>
<br>
<a href="http://nebc.nerc.ac.uk" target="_blank">http://nebc.nerc.ac.uk</a><br>
<a href="tel:%2B44%201491%2069%202705" value="+441491692705">+44 1491 69 2705</a><br>
</div><div class="HOEnZb"><div class="h5">_______________________________________________<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div>*********************************************<br>Md Tauqeer Alam, Ph.D<br>Division of Infectious Diseases</div><div>Emory University School of Medicine</div>
<div>615 Michael Street, Atlanta, GA 30322, USA</div><div><a href="mailto:tauqeer9@gmail.com" target="_blank">tauqeer9@gmail.com</a><br></div></div>
</div></div>