[ensembl-dev] Local V64 instalation

[Duarte Molha]

Thanks Ian

You are right  the api says 63.

But I am pretty sure I downloaded it from your current api page. It that
version still v63? This is very confusing.

I can checkout the CVS for release 64 ... but I think you should make it
clear for people that the version here:
http://www.ensembl.org/info/docs/api/api_installation.html

is really v63.

Best regards

Duarte

=========================
     Duarte Miguel Paulo Molha
         Tel: +447772111304
  Email: duartemolha at gmail.com
=========================


On 19 October 2011 10:32, ian Longden <ianl at ebi.ac.uk> wrote:

> Check
> /ensembl/v64/ensembl-api/ensembl/modules/Bio/EnsEMBL/ApiVersion.pm
>
> and make sure that this has:
> my $API_VERSION = 64;
>
>
> The script seems to think it is release 63. You may need to checkout
> from cvs release 64 again.
>
> -Ian.
>
>
> On Wed, Oct 19, 2011 at 10:25 AM, Duarte Molha <duartemolha at gmail.com>
> 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
> > species/group   homo_sapiens/cdna
> > database        homo_sapiens_cdna_63_37
> > host:port       ensembldb.ensembl.org:5306
> > species/group   homo_sapiens/vega
> > database        homo_sapiens_vega_63_37
> > host:port       ensembldb.ensembl.org:5306
> > species/group   homo_sapiens/otherfeatures
> > database        homo_sapiens_otherfeatures_63_37
> > host:port       ensembldb.ensembl.org:5306
> > species/group   homo_sapiens/variation
> > database        homo_sapiens_variation_63_37
> > host:port       ensembldb.ensembl.org:5306
> > species/group   homo_sapiens/funcgen
> > database        homo_sapiens_funcgen_63_37
> > host:port       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',
> >                         -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()
> >     );
> > }
> > _______________________________________________
> > Dev mailing list    Dev at ensembl.org
> > List admin (including subscribe/unsubscribe):
> > http://lists.ensembl.org/mailman/listinfo/dev
> > Ensembl Blog: http://www.ensembl.info/
> >
> >
>
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