[DAS] Configuring a valid MAPMASTER?

[Jonathan Warren]

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
>>>
>>>
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>>
>
>
> -- 
> 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: chris at compbio.dundee.ac.uk
> Tel: +44 (0)1382 388 721
>
> The University of Dundee is a registered Scottish charity, No:  
> SC015096
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.