[ensembl-dev] GO adaptor in latest ensemblgenomes release

Simon Andrews simon.andrews at babraham.ac.uk
Mon Feb 24 13:01:40 GMT 2014


I just double checked and I'm pretty sure the v75 code is coming down with the v74 branch:

$ wget "http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensemblgenomes-21-74&view=tar"
--2014-02-24 12:59:31--  http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensemblgenomes-21-74&view=tar
Resolving cvs.sanger.ac.uk... 193.62.203.92
Connecting to cvs.sanger.ac.uk|193.62.203.92|:80... connected.
HTTP request sent, awaiting response... 301 Moved
Location: /cgi-bin/viewvc.cgi/ensembl.tar.gz?pathrev=branch-ensemblgenomes-21-74&root=ensembl&view=tar [following]
--2014-02-24 12:59:31--  http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?pathrev=branch-ensemblgenomes-21-74&root=ensembl&view=tar
Connecting to cvs.sanger.ac.uk|193.62.203.92|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/octet-stream]
Saving to: "ensembl.tar.gz?pathrev=branch-ensemblgenomes-21-74&root=ensembl&view=tar"
2014-02-24 12:59:56 (429 KB/s) - "ensembl.tar.gz?pathrev=branch-ensemblgenomes-21-74&root=ensembl&view=tar" saved [10378469]

$ tar -xf ensembl.tar.gz\?pathrev\=branch-ensemblgenomes-21-74\&root\=ensembl\&view\=tar
$ ls ensembl/sql/*75*
ensembl/sql/patch_74_75_a.sql  ensembl/sql/patch_74_75_b.sql  ensembl/sql/patch_74_75_c.sql  ensembl/sql/patch_74_75_d.sql  ensembl/sql/patch_74_75_e.sql


-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Simon Andrews
Sent: 24 February 2014 12:50
To: Ensembl developers list
Subject: Re: [ensembl-dev] GO adaptor in latest ensemblgenomes release

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=ensem
>>>>bl&
>>>>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/B
>>>>ase
>>>>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/B
>>>>ase
>>>>Me
>>>> taContainer.pm
>>>> line 139.
>>>>
>>>> Any ideas?
>>>>
>>>> Thanks
>>>>
>>>> Simon.
>>>>
>>>> The Babraham Institute, Babraham Research Campus, Cambridge CB22
>>>> 3AT Registered Charity No. 1053902.
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>>
>> The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT
>>Registered Charity No. 1053902.
>> The information transmitted in this email is directed only to the
>>addressee. If you received this in error, please contact the sender
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>>
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_______________________________________________
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