[ensembl-dev] Local V64 instalation

[Beth Yates]

Hi Duarte,

Thank you for bringing this to our attention. We have a cron job that 
runs each night to generate the api tar ball. For release 64 we moved 
the website to new hardware unfortunately we forgot to switch the cron 
job off on the old hardware and turn it on on the new hardware. This has 
now been fixed and the correct files will be generated and updated on 
the FTP site overnight tonight.

Best regards,
Beth

Duarte Molha wrote:
> I am having issues using a local version of ensembl database.
>
> I have already installed both the v62 version and the v64 version of 
> the ensembl database and respective APIs.
>
> If I use v62 api I can query the database with no issues, using V64 
> api the registry does not seem to read the mySQL database.
>
> As a test I used the local v64 api to query the remote database and 
> pull out the tables it finds. Here are the ones I retrieve for Human:
>
> species/group   homo_sapiens/core
> database        homo_sapiens_core_63_37
> host:port       ensembldb.ensembl.org:5306 
> <http://ensembldb.ensembl.org:5306/>
>
> species/group   homo_sapiens/cdna
> database        homo_sapiens_cdna_63_37
> host:port       ensembldb.ensembl.org:5306 
> <http://ensembldb.ensembl.org:5306/>
>
> species/group   homo_sapiens/vega
> database        homo_sapiens_vega_63_37
> host:port       ensembldb.ensembl.org:5306 
> <http://ensembldb.ensembl.org:5306/>
>
> species/group   homo_sapiens/otherfeatures
> database        homo_sapiens_otherfeatures_63_37
> host:port       ensembldb.ensembl.org:5306 
> <http://ensembldb.ensembl.org:5306/>
>
> species/group   homo_sapiens/variation
> database        homo_sapiens_variation_63_37
> host:port       ensembldb.ensembl.org:5306 
> <http://ensembldb.ensembl.org:5306/>
>
> species/group   homo_sapiens/funcgen
> database        homo_sapiens_funcgen_63_37
> host:port       ensembldb.ensembl.org:5306 
> <http://ensembldb.ensembl.org:5306/>
>
>
> Why is this query pulling out V63 tables? Should it not be querying 
> the V64 tables instead? Is the current api on the server really v63 
> instead?
> I got the API from 
> : http://www.ensembl.org/info/docs/api/api_installation.html
>
> Your help is most appreciated.
>
> Best regards,
>
>      Duarte
>
> PS:  This is the script I used to query
>
> #!/usr/bin/perl -w
> #
> use strict;
>
> #Import Libs
> use lib '/ensembl/v64/ensembl-api/ensembl/modules'; # points to HG19 
> ensembl API
>
> #Use ENSEMBL modules
> use Bio::EnsEMBL::Registry;
>
> my $registry = 'Bio::EnsEMBL::Registry';
>
>
> #Create Registry for connecting to database
> $registry->load_registry_from_db( -host => 'ensembldb.ensembl.org 
> <http://ensembldb.ensembl.org/>',
>                         -user => 'anonymous');
>
> my @db_adaptors = @{ $registry->get_all_DBAdaptors() };
>
> foreach my $db_adaptor (@db_adaptors) {
>     my $db_connection = $db_adaptor->dbc();
>
>     printf(
>         "species/group\t%s/%s\ndatabase\t%s\nhost:port\t%s:%s\n\n",
>         $db_adaptor->species(),   $db_adaptor->group(),
>         $db_connection->dbname(), $db_connection->host(),
>         $db_connection->port()
>     );
> }
> ------------------------------------------------------------------------
>
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