[DAS] Configuring a valid MAPMASTER?

[Chris Cole]

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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>>>
>>
>>
>> --
>> 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
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>
> Jonathan Warren
> Senior Developer and DAS coordinator
> blog: http://biodasman.wordpress.com/
> jw12 at sanger.ac.uk
> 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: chris at compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096