[ensembl-dev] upgrade to version 60

[Bram De Wilde]

Bummer,

Apparently I had the version 61 of the code as was show by enabling the verbosity option, Thanx!!!

Strange enough though, because I had downloaded the code from the ensembl website ( http://www.ensembl.org/info/docs/api/api_installation.html ) where the hyperlink clearly suggests that I was downloading version 60... <a href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-60&view=tar">ensembl</a> possibly other people will get confused?...

Oh well, now I got a taste of the CVS way of installing I'm never going back, so thanx again. I got it all working now.

Kind regards,

Bram


On 26-dec-2010, at 20:23, Ian wrote:

> This only happens when the API and the database selected are not the same version.
> Use -verbose => 1 in load_registry_from_db to see what version it is trying to load.
> 
> It is usually best to delete the version of the API and install the new one as cvs can sometimes get confused when over writing.   
> 
> So if you get a new checkout and make sure this is in a new directory you should be okay.
> But add the verbose option to see what the registry is trying to do.
> 
> If the problem continues please let us know what the verbose option gives you.
> 
> Ian longden
> Ensembl developer.
> 
> On Dec 26, 2010, at 5:28 PM, Bram De Wilde <gbramdewilde at gmail.com> wrote:
> 
>> Hi everyone,
>> 
>> I just upgraded our install of the API from version 59 to 60 and all of my code stopped working.
>> I tracked down the problem to the registry not being able to connect to the database... I guess?... Or at least I get zero results back when I try to query the database.
>> This simple piece of test code works perfectly on my v59 install but stops working when I try and use the freshly installed v60:
>> 
>> require Bio::EnsEMBL::Registry;
>> my $registry = 'Bio::EnsEMBL::Registry'; 
>> 
>> $registry->load_registry_from_db(
>>     -host => 'ensembldb.ensembl.org',
>>     -user => 'anonymous',
>> 	-port => 5306,
>> );
>> 
>> 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()
>>     );
>> }
>> 
>> 
>> I receive no errors when I execute the code making this a hard problem to debug. Any kind of slice I try to get from any adaptor on my registry will return undefined . When I use the mysql client on my server: mysql -u anonymous -h ensembldb.ensembl.org -P 5306, and perfrom a show databases I get to see the database just fine: "homo_sapiens_core_60_37e" is in the list so the mysql connection does not seem to be the cause of all this.
>> 
>> Installation was done exactly as described in the online tutorial (the files from my v 59 and v60 install look exactly the same on my machine, with the correct permissions set...)
>> 
>> The perldoc for the Bio/EnsEMBL/Registry.pm does not mention any changes in the way we are supposed to connect to the database, nor does the online manual.
>> 
>> Anyone has any pointers as to what i am doing wrong?
>> 
>> Kind regards,
>> 
>> 
>> Bram De Wilde, MD
>> Center for Medical Genetics Ghent (CMGG)
>> Ghent University Hospital
>> Medical Research Building (MRB), 2nd floor, room 120.050
>> De Pintelaan 185, B-9000 Ghent, Belgium
>> +32 9 332 4812 (phone) | +32 9 332 6549 (fax)
>> http://medgen.ugent.be/
>> Bram.DeWilde at UGent.be 
>> 
>> 
>> 
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev

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