[ensembl-dev] Region report tool / Registry - only works for mysql users without password?
ktaylor at ebi.ac.uk
Mon Apr 30 16:28:20 BST 2012
Hi Nick, I'm glad to see someone is using the Region report tool from
the command line.
There is a bug that we know of in the secondary host connection code,
which is being fixed, but there are a couple of things we have noticed
in your parameter specification.
Firstly, pointing the tool at the same server twice redundant. The
feature is in place to assist in situations (such as on our main public
servers) where data must be spread across several hosts. Hopefully you
are just masking your true connection settings.
Secondly, MySQL behaves badly with "localhost" as a target. It tends to
assume socket connections instead of by http, which can cause no end of
connection issues. Sockets are treated differently for valid users and
authentication than through HTTP. Try feeding it 127.0.0.1 as a host
On 30/04/12 16:00, Nick Langridge wrote:
> I'm trying to use the region report tool but it seems to ignore the
> mysql password that I supply in the options:
> perl region_report.pl --species=Anopheles_gambiae --input=/tmp/inputfile
> --include=gt --report --host=localhost --port=3306 --db_version=66
> --user=myuser --password=mypass --secondaryhost=localhost
> --secondaryport=3306 --db_version=66 --secondaryuser=myuser
> --secondarypassword=mypass --output=/tmp/outputfile
> I see error:
> connect: DBI:mysql:host=localhost;port=3306 myuser at
> line 1566.
> DBI connect('host=localhost;port=3306','myuser',...) failed: Access
> denied for user 'myuser'@'localhost' (using password: NO) at
> line 1567
> -------------------- EXCEPTION --------------------
> MSG: Cannot connect to the Ensembl MySQL server at localhost:3306; check
> your settings & DBI error message: Access denied for user
> 'myuser'@'localhost' (using password: NO)
> STACK Bio::EnsEMBL::Registry::load_registry_from_db
> STACK Bio::EnsEMBL::Registry::load_registry_from_multiple_dbs
> STACK toplevel
> Ensembl API version = 66
> As far as I can see, the region report script calls
> Bio::Ensembl::Registry->load_registry_from_multiple_dbs() with the
> password present, but the registry seems to ignore it.
> Is this the expected behaviour?
> Dev mailing list Dev at ensembl.org
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