[ensembl-dev] VM 75

[Genomeo Dev]

Hi,

I was using useastdb.ensembl.org. ensembldb.ensembl.org works but is
heavily slow at the moment.

Thanks


On 28 February 2014 12:04, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:

> Hi,
>
> This error is commonly caused by absent databases. If you're not using
> ensembldb.ensembl.org, then you may not have release 75 databases
> available for Human and others on your server of choice.
>
> Our master copy of the VM checks out ok. Please investigate your
> configuration, to see whether you need to aim for a server that contains
> release 75.
>
>
> Regards,
>
> Kieron Taylor
>
> Ensembl Core
>
>
> On 28/02/2014 10:26, Genomeo Dev wrote:
>
>> Hi,
>>
>> I just loaded the new release VM 75.
>>
>> ~/verify-installation worked fine.
>>
>> But:
>>
>> use Bio::EnsEMBL::Registry;
>> my $registry = 'Bio::EnsEMBL::Registry';
>> my $gene_adaptor  = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
>>
>> gives me this error:
>>
>> -------------------- WARNING ----------------------
>> MSG: Human is not a valid species name (check DB and API version)
>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1198
>> CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 983
>> Date (localtime)    = Fri Feb 28 10:20:41 2014
>> Ensembl API version = 75
>> ---------------------------------------------------
>>
>> -------------------- EXCEPTION --------------------
>> MSG: Can not find internal name for species 'Human'
>> STACK Bio::EnsEMBL::Registry::get_adaptor
>> /home/ensembl/ensembl-api-folder/ensembl/modules/Bio/
>> EnsEMBL/Registry.pm:985
>> STACK toplevel ./fetch_ensembl_genes_v3b.pl:71
>> <http://fetch_ensembl_genes_v3b.pl:71>
>>
>> Date (localtime)    = Fri Feb 28 10:20:41 2014
>> Ensembl API version = 75
>> ---------------------------------------------------
>>
>> Any suggestions please?
>>
>> --
>> G.
>>
>
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-- 
G.
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