[ensembl-dev] VM 75

[Harpreet Riat]

Hi,

The 75 databases are now there on useastdb.ensembl.org.

Thanks,
Harpreet


On 28 Feb 2014, at 12:51, Steve Trevanion wrote:

> Hi,
> 
> Apologies, the 75 databases are not yet on useastdb. We'll let you know as soon as they are.
> 
> Regards,
> 
> Steve
> 
> On 28/02/2014 12:39, Genomeo Dev wrote:
>> 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.
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>> 
>> 
>> 
>> -- 
>> G.
>> 
>> 
>> _______________________________________________
>> Dev mailing list    
>> Dev at ensembl.org
>> 
>> Posting guidelines and subscribe/unsubscribe info: 
>> http://lists.ensembl.org/mailman/listinfo/dev
>> 
>> Ensembl Blog: 
>> http://www.ensembl.info/
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/