[ensembl-dev] Checking the branch version from the API

[Andy Yates]

Hi Giuseppe,

Thanks for bringing out a CPAN module based on our data. It's good to see that it is being used :)

With respect to your API concerns you shouldn't worry about this too much. It is possible to connect to a release 58 Ensembl Genomes database with the Ensembl 58 API. The reason why we make the different branch available is to push in bug fixes to the code which could cause problems with Ensembl & require more engineering to make a suitable bug fix or when Ensembl do not see a bug with their data & they are, quite rightly, reluctant to introduce unnecessary code, as they see it, into their stable branches.

You can load from both resources using the following command in any API version.

Bio::EnsEMBL::Registry->load_registry_from_multiple_dbs(
  { -host =>  'mysql.ebi.ac.uk', -port =>  4157, -user =>  'anonymous' },
  { -host =>  'ensembldb.ensembl.org', -port =>  5306, -user =>  'anonymous' }
);

For compara both API branches should work with either release e.g. Ensembl's 59 API branch will work with EnsemblGenomes' upcoming release 6 & vica-versa.

So long as there is an Ensembl API available on the user's PERL5LIB or @INC then I'd just use it :)

As to the question about licensing rules I'll leave that to the Ensembl team to answer.

Andy

On 26 Aug 2010, at 17:16, Giuseppe Gallone wrote:

> Hi Andy,
> 
> I'm writing a Perl module, which should be shortly released on CPAN, that requires installation of either set of APIs as a prerequisite (depending on the interest of the final user: vertebrates vs. vertebrates+metazoa).
> 
> I'm writing some perl test cases and need to account for the two different branches ('multi' and 'metazoa') when testing the connection through the registry. The thing is, if a user has installed the standard branch only, the registry connection to 'metazoa' will obviously fail. Hence the question. Is there a way through this?
> 
> BTW are there any obvious licensing rules I should be aware of when calling some Ensembl API methods through my CPAN module (GNU license)?
> 
> Best regards
> Giuseppe
> 
> On 26/08/10 17:11, Andy Yates wrote:
>> Hi Giuseppe,
>> 
>> I'm sorry to say this that there is no way to know this from the API side. Why do you need to know this?
>> 
>> Andy
>> 
>> On 26 Aug 2010, at 16:59, Giuseppe Gallone wrote:
>> 
>>> Hello,
>>> 
>>> apologies if my question has been answered elsewhere. Is there a way to check, using the API, what's the branch of the API itself? In other words I'd like to know within my script if what I have is the normal branch (eg branch-ensembl-59) or the genomes branch (eg branch-ensemblgenomes-5-58). Thanks!
>>> 
>>> 
>>> Best,
>>> Giuseppe
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>>> 
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>> 
> 
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> 
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/