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

Andy Jenkinson andy.jenkinson at ebi.ac.uk
Tue Nov 9 17:59:32 GMT 2010


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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