[ensembl-dev] adding a new specie

[oreetseng at sanbi.ac.za]

Hi Anne,

The first part is fixed (search on the front page), i have also added the
species.ensembl_alias_name value, I still get the same complaint, with the
specie name not appearing:

"multi is not a valid species name for this instance
Use of uninitialized value $common in hash element at
fungi/eg-plugins/common/modules/EnsEMBL/Web/Document/HTML/SpeciesPage.pm
line 39"

I am proof checking the modifications made to the files and will keep you
posted,

Thanx a lot!!
Oreetseng




> 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
>
>
>
>
>
> --
>  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.
>