[ensembl-dev] unavailable Ensembl 'Comparative Genomics' funnction with release 63 (Anne Parker)

[Steve Moss]

Dear Daniel,

Yes, this is indeed a MySQL problem! Perhaps you are using the wrong
username or password? This is the error that MySQL throws when there is an
authentication issue.

If you change your script to use the following, you should see there are no
issues:

use Bio::EnsEMBL::Registry;
> my $registry = 'Bio::EnsEMBL::Registry';
> $registry->load_registry_from_db( -host => 'useastdb.ensembl.org', -user
> => 'anonymous', -port => 5306);


Have a play with your MySQL settings on the command line and then update
your script accordingly if this is the case

mysql -h 192.168.20.19 -u root --password=mypass -P3306


It may be that you have limited the root login to hosts matching locahost/
127.0.0.1 only, and you may need to include 192.168.20.0/24 to allow access
from the subnet or just your 192.168.20.25 host?

Cheers,

Steve

On 14 September 2011 12:00, <dev-request at ensembl.org> wrote:

> Message: 1
> Date: Wed, 14 Sep 2011 09:36:33 +0100
> From: Anne Parker <ap5 at sanger.ac.uk>
> Subject: Re: [ensembl-dev] unavailable Ensembl 'Comparative Genomics'
>        funnction with release 63
> To: ?? <danielchen06 at gmail.com>
> Cc: Ensembl dev list <dev at ensembl.org>
> Message-ID: <2001680B-E04A-492D-97BC-776954B40F73 at sanger.ac.uk>
> Content-Type: text/plain; charset=utf-8
>
> This is a MySQL permissions problem, I think, not anything to do with
> Ensembl:
>
> > Access denied for user 'root'@'192.168.20.25' (using password: YES)
>
> Can you connect to these databases from the command line, using the root
> user and password?
>
> Cheers
>
> Anne
>

-- 
*Steve Moss*
PhD Research Student
Evolutionary Biology Group
Department of Biological Sciences
University of Hull
Cottingham Road
Hull, HU6 7RX

Evolution site: http://goo.gl/7ZReN
<http://www2.hull.ac.uk/science/biological_sciences/research/evolutionary_biology.aspx>Work
site: http://goo.gl/LzGQo
Personal site: http://stevemoss.ath.cx/
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