[ensembl-dev] Region report tool / Registry - only works for mysql users without password?

[Nick Langridge]

Hi,

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 
/ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm 
line 1566.
DBI connect('host=localhost;port=3306','myuser',...) failed: Access 
denied for user 'myuser'@'localhost' (using password: NO) at 
/ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm 
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 
/ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm:1567
STACK Bio::EnsEMBL::Registry::load_registry_from_multiple_dbs 
/ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm:2296
STACK toplevel 
/ensembl/www-live/VB-2012-03/ensembl-tools/scripts/region_reporter/region_report.pl:176
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?

Cheers,
Nick