On 23 Jan 2007, at 15:28, Camargo R D S wrote:
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.
Hi Arek,
I've tried that before, changed the file again:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation
name = "ensembl_mart_42"
displayName = "My ensembl_mart_42 Database"
databaseType = "mysql"
host = "localhost"
port = "3306"
database = "ensembl_mart_42"
schema = "ensembl_mart_42"
user = "root"
password = "mysql"
visible = "1"
default = ""
includeDatasets = ""
/>
</MartRegistry>
Just a question, how BioMart will be able to find my local data that
is in a
complete different directory? Sorry about my silly question.
no problem but I am a bit confused here. Can you actually
connect to your database using mysql client?
ei can you do
mysql -uroot -hlocalhost ensembl_mart_42
and see mart tables? if you can the software will also be able to
The error below suggests that you have at least 'meta' table missing
from there. Can you try the command above and on mysql prompt
say
'show tables'
and tell me what you are seeing?
cheers,
a/
After I changed MyRegistry.xml file I re-run configure.pl and got the
following message:
[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
DBD::mysql::st execute failed: Table
'ensembl_mart_42.meta_conf__user__dm'
doesn't exist
at
/home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Configuration/
MartDBLocation.pm
line 203.
DBD::mysql::st execute failed:
Table 'ensembl_mart_42.meta_conf__dataset__main' doesn't exist
at
/home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Configuration/
MartDBLocation.pm
line 264.
WARNING: Could not fetch Configuration XML for :My ensembl_mart_42
Database
Table 'ensembl_mart_42.meta_conf__dataset__main' doesn't exist
SKIPPING
ERROR something wrong with your registry: Could not fetch
Configuration XML
for : My ensembl_mart_42 Database
Table 'ensembl_mart_42.meta_conf__dataset__main' doesn't exist
++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++
++++++++++++ I checked whether I had that file and I found:
/home/renata/BioMart/data/mysql/ensembl_mart_42/
meta_conf__user__dm.txt.table
/home/renata/BioMart/data/mysql/snp_mart_42/
meta_conf__user__dm.txt.table
/home/renata/BioMart/data/mysql/vega_mart_42/
meta_conf__user__dm.txt.table
/home/renata/BioMart/data/mysql/sequence_mart_42/
meta_conf__user__dm.txt.table
/home/renata/BioMart/data/mysql/compara_mart_homology_42/
meta_conf__user__dm.txt.table
/home/renata/BioMart/data/mysql/compara_mart_multiple_ga_42/
meta_conf__user__dm.txt.table
/home/renata/BioMart/data/mysql/compara_mart_pairwise_ga_42/
meta_conf__user__dm.txt.table
++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++
Trace begun
at
/home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Configuration/
MartDBLocation.pm
line 272
BioMart::Configuration::MartDBLocation::
_retrieveDatasetInfo('BioMart::Configuration::
MartDBLocation=HASH(0x93cc294)', 'default',
0) called
at
/home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Configuration/
Location.pm
line 574
BioMart::Configuration::Location::retrieveDatasetInfo('BioMart::
Configuration::MartDBLocation=HASH(0x93cc294)', 'default',
0) called
at /home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line
1153
BioMart::Initializer::_populateRegistry('BioMart::
Initializer=HASH(0x93335d0)')
called at
/home/renata/BioMart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 244
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
Thank you !
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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