[ensembl-dev] Error connecting to MySQL

Andy Yates ayates at ebi.ac.uk
Wed Dec 18 12:32:32 GMT 2013


Hi there,

Our developers have been looking at this issue with the VM and they have been unable to replicate the issue. However it seems that the script is being overzealous in calling a problem with the DBI module installation. You can verify this with the following command

perl -MDBI -e 'warn $DBI::VERSION'

In actual fact we believe this to be an issue with your local firewall possibly. Could you contact your systems admin and make sure the correct ports are open (3306). Also you can follow the guide on debugging an installation from http://www.ensembl.org/info/docs/api/debug_installation_guide.html. Whilst the sections on installing code is not relevant to you sections 4 (Try Connecting to Ensembl Using a MySQL Client) onwards will be.

Hope this helps,

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 13 Dec 2013, at 17:30, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi all,
> 
> I am getting the error below when verifying installation of the Ensembl VM 73 (same error with version 74).
> 
> Any suggestions?
> 
> Genomeo
> 
> ensembl at ensembl:~$ ./verify-installation 
> DBI connect('host=ensembldb.ensembl.org;port=5306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110) at /home/ensembl/ensembl-api-folder/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1607
> ERROR: Error detected when connecting to Ensembl!
> 	Cannot find the DBI perl module. Please install this using your package management system, cpan or cpanm. Please consult http://www.ensembl.org/info/docs/api/api_installation.html
> 	Cannot seem to contact EnsemblDB at 'ensembldb.ensembl.org' with the username 'anonymous'. Try running 'ping ensembldb.ensembl.org' or asking your systems about firewalls against port 5306
> ================================================================================
> If the problem persists please send the following error message to helpdesk at ensembl.org
> 
> -------------------- EXCEPTION --------------------
> MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:5306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110)
> STACK Bio::EnsEMBL::Registry::load_registry_from_db /home/ensembl/ensembl-api-folder/ensembl/modules/Bio/EnsEMBL/Registry.pm:1607
> STACK (eval) ./verify-installation:110
> STACK toplevel ./verify-installation:101
> Date (localtime)    = Fri Dec 13 15:21:56 2013
> Ensembl API version = 73
> ---------------------------------------------------
> ================================================================================
> 
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