[ensembl-dev] GO adaptor in latest ensemblgenomes release

Simon Andrews simon.andrews at babraham.ac.uk
Mon Feb 24 12:49:42 GMT 2014


Hi Andy,

Yes, I did use wget, but I quoted the URL so the & wasn’t interpreted by
the shell so I don’t think it’s that.

Simon.

On 24/02/2014 12:17, "Andy Yates" <ayates at ebi.ac.uk> wrote:

>Hi Simon,
>
>When you retrieved the code from CVS did you use wget? If you did you may
>have fallen into the old trap of the command line seeing the & in the
>middle of the URL and assuming you wanted to fork the download. Something
>like this should work:
>
>wget
>'http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&on
>ly_with_tag=branch-ensemblgenomes-21-74&view=tar'
>
>Andy
>
>------------
>Andrew Yates - Ensembl Support Coordinator
>European Bioinformatics Institute (EMBL-EBI)
>European Molecular Biology Laboratory
>Wellcome Trust Genome Campus
>Hinxton
>Cambridge CB10 1SD
>Tel: +44-(0)1223-492538
>Fax: +44-(0)1223-494468
>http://www.ensembl.org/
>
>On 24 Feb 2014, at 12:13, Simon Andrews <simon.andrews at babraham.ac.uk>
>wrote:
>
>> Thanks - I¹d forgotten that was there, I think that was supposed to be a
>> temporary fix for a previous problem I had.
>>
>> I¹m now getting a warning that there is a difference between the
>>software
>> release (75) and database release (74).  I included the URL I used below
>> which definitely says that it¹s the v74 branch.  Is this a problem?
>>Could
>> some new code have been checked into the wrong branch?
>>
>> Thanks
>>
>> Simon.
>>
>> On 24/02/2014 12:02, "ek" <ek at ebi.ac.uk> wrote:
>>
>>> to use the latest code
>>>
>>> -DBNAME => 'ensemblgenomes_ontology_10_63',
>>>
>>> should be
>>>
>>> -DBNAME => 'ensemblgenomes_ontology_21_74',
>>>
>>> regards
>>>
>>> Eugene
>>>
>>> On 2014-02-24 11:57, Simon Andrews wrote:
>>>> The latest ensemblgenomes release (just downloaded from the website -
>>>>
>>>>
>>>>http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&
>>>>on
>>>> ly_with_tag=branch-ensemblgenomes-21-74&view=tar)
>>>> doesn't allow me to get a GO adapter to use in our scripts.
>>>>
>>>> #!/usr/bin/perl
>>>> use warnings;
>>>> use strict;
>>>> use lib ("/home/andrewss/EnsemblAPI/bioperl-live");
>>>> use lib ("/home/andrewss/EnsemblAPI/plants/ensembl/modules");
>>>> use Bio::EnsEMBL::Registry;
>>>> use Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
>>>>
>>>> warn "Loading Registry information - please be patient\n";
>>>>
>>>>  my $registry = 'Bio::EnsEMBL::Registry';
>>>>
>>>>  $registry->load_registry_from_db(
>>>>                                 -host => 'mysql.ebi.ac.uk',
>>>>                                 -port => 4157,
>>>>                                 -user => 'anonymous'
>>>>                                );
>>>>
>>>> #  $registry -> set_disconnect_when_inactive(1);
>>>>
>>>>  my $ontology_dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor -> new (
>>>>
>>>> -SPECIES => 'Multi',
>>>>
>>>> -GROUP => 'ontology',
>>>>
>>>> -HOST => 'mysql.ebi.ac.uk',
>>>>
>>>> -PORT => 4157,
>>>>
>>>> -USER => 'anonymous',
>>>>
>>>> -DBNAME => 'ensemblgenomes_ontology_10_63',
>>>>                                                                   );
>>>>
>>>> my $GO_adapter =   $registry->get_adaptor( 'Multi', 'Ontology',
>>>> 'GOTerm' );
>>>>
>>>> DBD::mysql::st execute failed: Unknown column 'species_id' in 'where
>>>> clause' at
>>>>
>>>>
>>>>/home/andrewss/EnsemblAPI/plants/ensembl/modules/Bio/EnsEMBL/DBSQL/Base
>>>>Me
>>>> taContainer.pm
>>>> line 139.
>>>> DBD::mysql::st execute failed: Unknown column 'species_id' in 'where
>>>> clause' at
>>>>
>>>>
>>>>/home/andrewss/EnsemblAPI/plants/ensembl/modules/Bio/EnsEMBL/DBSQL/Base
>>>>Me
>>>> taContainer.pm
>>>> line 139.
>>>>
>>>> Any ideas?
>>>>
>>>> Thanks
>>>>
>>>> Simon.
>>>>
>>>> The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT
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