[ensembl-dev] Attaching DAS, species not found error

[Ken Youens-Clark]

Andy,

You're right, my coordinates were messed up for several species.  They're not all perfect, but I hacked my registry_coordinates.xml file to change "MSU_6,Chromosome,Oryza sativa japonica" to "MSU_6,Chromosome,Oryza sativa" since our japonica browser has to be called "Oryza_sativa."  The first is actually more correct, but there really seems to be a problem with DAS handling the trinomial names -- it's also a problem for our "Oryza sativa indica" browser which we have to call just "Oryza_indica."  

So now this looks like it /should/ work:

	http://www.gramene.org/gramenedas/das/sources

But I still get the same error with "Oryza_sativa" not being found.  Out of curiousity, I also added "organism = Oryza sativa" to one of my sources, but that didn't help, either.

Gramene is using Ensembl v59 right now.

Any suggestions?

ky

On Nov 9, 2010, at 10:59 AM, Andy Jenkinson wrote:

> Hi Ken,
> 
> At first glance: your DAS server does not report any coordinate systems for the Oryza (and others) sources, like it does for some other species'. Ensembl therefore doesn't know that they are for Oryza. If you need to add suitable coordinate systems to the registry, an admin of the DAS Registry can help (me included).
> 
> But actually, the behaviour you describe does not reflect what happens on the main Ensembl site. If the source has no coordinate systems, here they are still listed but simply ask you to specify the correct coordinate system. This seems to work, so the problem may be specific to gramene. Take a look at:
> ensembl-webcode/modules/EnsEMBL/Web/Object/UserData.pm
> ensembl-external/modules/Bio::EnsEMBL/ExternalData/DAS/SourceParser.pm
> 
> Which version of Ensembl is gramene based on?
> 
> Cheers,
> Andy
> 
> On 9 Nov 2010, at 16:19, Ken Youens-Clark wrote:
> 
>>> From Gramene's rice browser (Oryza sativa japonica):
>> 
>> 	http://dev.gramene.org/Oryza_sativa/Location/View?r=1:8001-18000
>> 
>> I try to attach a DAS track via "Manage your data" -> "Attach DAS" and specifying "http://dev.gramene.org/gramenedas/das" as the URL, I get this error:
>> 
>> 	Unable to access DAS source. Server response: No Oryza_sativa DAS sources found for http://dev.gramene.org/gramenedas/das
>> 
>> But if I look here:
>> 
>> 	http://dev.gramene.org/gramenedas/das/sources
>> 
>> I do see "Oryza_sativa" sources.  How or where exactly is the browser looking for "Oryza_sativa" to know what it can display?
>> 
>> --
>> Ken Youens-Clark
>> kclark at cshl.edu
>> Gramene.org Project Manager
>> Ware Lab/CSHL/USDA-ARS
>> 
>> 
>> _______________________________________________
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> 

--
Ken Youens-Clark
kclark at cshl.edu
Gramene.org Project Manager
Ware Lab/CSHL/USDA-ARS