Useful to know. Thanks.
On 07/02/11 14:59, Jonathan Warren wrote:
I've put a Andys previous answer to this question (when I asked it)
here:
http://biodasman.wordpress.com/2010/12/06/implementing-types-in-proserver/
On 7 Feb 2011, at 14:48, Chris Cole wrote:
Hi Andy,
Thanks for the help. Looks like I was close...
I now get an error regarding the 'types' command. I haven't
implemented it so that's not a surprise. However, I'm struggling to
find documentation on the build_types() function and what data it
should return. My source data only has one type: 'expression_tag' so
how should I return that?
Cheers,
Chris
On 07/02/11 11:40, Andy Jenkinson wrote:
Hi Chris,
The 'reference' Ensembl sources are suitable for use as mapmasters,
as they provide sequence information:
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
So, barring any particular nuance of IGB, the correct mapmaster URL
would be:
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
(assuming thaliana)
The reason for all this is I guess that IGB does not support the DAS
1.53E/1.6 sources command, which provides species and coordinate
information directly.
Cheers,
Andy
On 7 Feb 2011, at 10:34, Chris Cole wrote:
Hi,
I have a functioning ProServer install that works fine with Ensembl,
but I'd like to get it working with IGB as well. However, it fails
to load as it has a 'Missing MAPMASTER element'. I see I need to
specify a URI to a known MAPMASTER source, but I've no idea how.
The server is for Arabidopsis data and I've found the Ensembl DAS
sources for plants, but which can I use as a mapmaster?
http://plants.ensembl.org/das/dsn
Or am I barking up the wrong tree?
Any pointers much appreciated.
Cheers,
Chris
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Jonathan Warren
Senior Developer and DAS coordinator
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Ext: 2314
Telephone: 01223 492314
--
Dr Chris Cole
Senior Bioinformatics Research Officer
College of Life Sciences
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK
url: http://network.nature.com/profile/drchriscole
e-mail: [email protected]
Tel: +44 (0)1382 388 721
The University of Dundee is a registered Scottish charity, No: SC015096
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