[Bioperl-l] populating gbrowse with genomic data rapidly

Liam Elbourne lelbourn at cbms.mq.edu.au
Thu May 14 22:48:44 EDT 2009

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  

  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!



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

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