[Bioperl-l] Fwd: populating gbrowse with genomic data rapidly

Liam Elbourne lelbourn at cbms.mq.edu.au
Fri May 15 01:57:09 EDT 2009

Hi All,

Quel embarrassment, I just found the highly esteemed Dr Stein's http://search.cpan.org/~lds/GBrowse-1.993/docs/pod/GENBANK_HOWTO.pod 
  which is exactly what I asked for. Sorry for spamming everybody on  
the list!

Google first, ask questions later...


Begin forwarded message:

> From: Liam Elbourne <lelbourn at cbms.mq.edu.au>
> Date: 15 May 2009 12:48:44 PM
> To: Lincoln Stein <lincoln.stein at gmail.com>
> Cc: BioPerl List <bioperl-l at lists.open-bio.org>
> Subject: populating gbrowse with genomic data rapidly
> Hi Lincoln (and all),
> This is really a gbrowse specific, and not a particularly bioperly  
> question, but I'm not on a gbrowse list, and I figured other bioperl  
> people were likeliest to know how to help.
> I've (to all appearances) completely successfully installed  
> gbrowse(2.0), with some minor glitches mainly caused by typos in the  
> instructions, which I will pass on in due course. The demo data  
> looks great.
> I've been asked (spelt begged, ordered, requested, commanded) if at  
> all possible to get about 6/7 genomes available for browsing by  
> Sunday (USA time) for a meeting. I've skimmed the tutorial (which  
> looks excellent, thank you Lincoln!) and started working through it,  
> but wondered if somewhere there was a cheat sheet or "Dummies guide  
> to stuffing gbrowse full of Genome Data" that would allow me to get  
> these genomes up by then. I know there is a script for converting  
> genbank data to gff, which will get me part of the way there, as  
> most or all of the genomes have annotation in genbank format, so  
> from my attempts to date (yesterday afternoon) I would say that what  
> I need is:
> * appropriately setup .conf files
> * and instructions on how the data needs to formatted (ie what has  
> to go into the gff files)  named and located (presumably all in the  
> "databases" directory), in order to 'match' the .conf files.
> Absolutely any assistance would be appreciated, including "it's  
> completely impossible, give up now!" or I guess potentially "it's  
> all in the instructions", which I'm sure it is...  I apologise in  
> advance if there is already a short guide available on the GMOD wiki  
> or elsewhere that I have missed, and will happily thank whoever will  
> point me towards it!
> Regards,
> Liam.
> ______________________________
> Dr Liam Elbourne
> Research Fellow (Bioinformatics)
> Paulsen Laboratory
> Macquarie University
> Sydney
> Australia.


Dr Liam Elbourne
Research Fellow (Bioinformatics)
Paulsen Laboratory
Macquarie University

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