[ensembl-dev] adding a new specie

[Anne Parker]

On 8 Nov 2011, at 15:02, oreetseng at sanbi.ac.za wrote:

> 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"

As this is in the EnsemblGenomes plugin, I don't have immediate access to a copy, and don't know what changes the EG team have made. Perhaps you could contact them if the problem persists?

One final thought - if you've changed the database, you need to delete the .db.packed file as well as config.packed when you restart your server.

Cheers

Anne

> 
> 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.
>> 
> 
> 

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