[ensembl-dev] adding a new specie

Anne Parker ap5 at sanger.ac.uk
Tue Nov 8 09:32:45 GMT 2011


Hi Oreetseng

It looks as though your species configuration is incomplete somewhere.

On 7 Nov 2011, at 17:52, oreetseng at sanbi.ac.za wrote:

> Hi all ,
> 
> I want to add a new specie to the ensembl local core database, i have
> configured all the important files as per ensembl documentation guide.
> 
> On the front page the local mirror, my_specie picture shows, but unlike
> other fungal species there is no name next to the picture and when i click
> on the picture the error appears that reads: "Search
> .Runtime Error in component "EnsEMBL::Web::Component::Info::Summary
> [content]"
> Function EnsEMBL::Web::Component::Info::Summary fails to execute due to
> the following error:
> Can't use an undefined value as a HASH reference at
> fungi/modules/EnsEMBL/Web/Document/HTML/HomeSearch.pm line 80 "

Please compare the .ini file for your new species to the Ensembl ones - at the end of the file there should be a block defining sample entry points. Here's the equivalent for yeast:

[SAMPLE_DATA]
LOCATION_PARAM    = IV:366098-466099
LOCATION_TEXT     = IV:366098-466099

GENE_PARAM        = YGR147C
GENE_TEXT         = NAT2

TRANSCRIPT_PARAM  = YGR147C
TRANSCRIPT_TEXT   = NAT2

VARIATION_PARAM   = s02-316976
VARIATION_TEXT    = s02-316976

SEARCH_TEXT       = alcohol dehydrogenase

I will fix the code so that absence of this data does not cause an error, but I recommend populating these values anyway.

> 
> on the taillog the error reads as follows:
> multi is not a valid species name for this instance
> Can't use an undefined value as a HASH reference at
> /fungi/modules/EnsEMBL/Web/Document/HTML/HomeSearch.pm line 80.
> Use of uninitialized value $common in hash element at
> fungi/eg-plugins/common/modules/EnsEMBL/Web/Document/HTML/SpeciesPage.pm
> line 39.


The error here seems to be that no common name is being picked up by the web code (hence the absence of a link next to the picture). Please check that your database contains a meta entry called species.ensembl_alias_name - the value can be the scientific name or the common name, whichever you prefer to display. 

Let me know how you get on.

Cheers

Anne


Anne Parker
Ensembl Web Production Manager
http://www.ensembl.org







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