On 23 Jan 2007, at 14:34, Camargo R D S wrote:
Dear Arek,
I downloaded the ensembl databases that are in the BioMart format:
compara_mart_homology_42
cmpara_mart_multiple_ga_42
compara_mart_pairwise_ga_42
snp_mart_42
sequence_mart_42
vega_mart_42
ensembl_mart_42
But I don't know how to set my Registry to be able to see them.
I am able to see the databases at martdb.ebi.ac.uk, that are exactly
the same,
but I need them locally.
so:
/home/renata/BioMart/biomart-perl/conf/
contain MyRegistry.xml
but my data is at:
/home/renata/BioMart/data/mysql/
MyRegistry.xml is
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation
name = "ensembl_mart_42"
displayName = "My ensembl_mart_42 Database"
databaseType = "/usr/bin/X11/mysql"
host = "localhost"
port = "3306"
database = "/home/renata/BioMart/data/mysql/ensembl_mart_42/"
schema = "/home/renata/BioMart/data/mysql/ensembl_mart_42/"
user = "root"
password = "mysql"
visible = "1"
default = ""
includeDatasets = ""
/>
</MartRegistry>
The message that I am getting is:
Hi Renata,
you need to change the 'databaseType' to 'mysql' not
"/usr/bin/X11/mysql"
as you have it at the moment. Similarily for 'database' and 'schema'
you simply need 'enembl_mart_42' not
'/home/renata/BioMart/data/mysql/ensembl_mart_42/'
For other databases you simply replicate your MartDBLocation changing
database and schema to 'compara_mart_homology_42',
'compara_mart_multiple_alignement_42' etc
hope that helps,
a.
[EMAIL PROTECTED]:/home/renata/BioMart/biomart-perl# perl bin/configure.pl -r
conf/MyRegistry.xml
Do you want to install in API only mode [y/n] [n]: n
Checking prerequisites ...[Looks good]
DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]: y
Cached Registry Unavailable...
Running Complete Clean...
Optional setting for martUser in MartDBLocation
location:ensembl_mart_42 not
defined - setting to default values
unsupported RDBMS
type:
"BioMart::Configuration::MartDBLocation=HASH(0x93cc454)->databaseType"
-
please use the correct name or supported RDBMS ...... skipping
connection
at
/home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Configuration/
DBLocation.pm
line 90.
COULD NOT CONNECT TO
DATABASE /home/renata/BioMart/data/mysql/ensembl_mart_42/.CHECK YOUR
SETTINGS
ERROR something wrong with your registry: Problems with the retrieval
of
dataset configuration
Please check:
that your mart Registry files contains correct
connection
params,
that you are using the correct version on XML::Simple,
that BioMart databases contain a populated meta_conf
tables
and
that you have set martUser correctly if you are running
in
restricted data
access mode (populated meta_conf__user__dm)
Trace begun
at /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line
270
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x93335d0)',
'registryFile',
'/home/renata/BioMart/biomart-perl/conf/MyRegistry.xml', 'action',
'cached', 'mode', 'memory')
called at
/home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 393
BioMart::Initializer::init_clean('BioMart::
Initializer=HASH(0x93335d0)', 'registryFile',
'/home/renata/BioMart/biomart-perl/conf/MyRegistry.xml', 'action',
'cached', 'mode', 'memory')
called at
/home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 344
BioMart::Initializer::init_cached('BioMart::
Initializer=HASH(0x93335d0)', 'registryFile',
'/home/renata/BioMart/biomart-perl/conf/MyRegistry.xml', 'action',
'cached', 'mode', 'memory')
called at
/home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 184
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x93335d0)',
'registryFile',
'/home/renata/BioMart/biomart-perl/conf/MyRegistry.xml', 'action',
'cached', 'mode', 'memory')
called at
/home/renata/BioMart/biomart-perl/bin/../lib/BioMart/RootI.pm line
42
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/renata/BioMart/biomart-perl/conf/MyRegistry.xml', 'action',
'cached', 'mode', 'memory')
called at /home/renata/BioMart/biomart-perl/bin/configureBioMart.pl
line 339
eval {...} at
/home/renata/BioMart/biomart-perl/bin/configureBioMart.pl line
338
[EMAIL PROTECTED]:/home/renata/BioMart/biomart-perl#
Thank you ever so much, Renata.
------------------------------------------------------------------------
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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