[Bioperl-l] populating gbrowse with genomic data rapidly
Liam Elbourne
lelbourn at cbms.mq.edu.au
Fri May 15 02:48:44 UTC 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
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.
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