[ensembl-dev] VM 75

[Kieron Taylor]

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.