Hi,
I am in the process of setting up a new BioMart server on a Linux machine.
I have worked through the installation procedure and run:
perl bin/configure.pl -r conf/registryURLPointer.xml
All works just fine. Then I tried to use my own configuration file:
perl bin/configure.pl --clean -r conf/reactome.xml
...and I got this:
COULD NOT CONNECT TO DATABASE msd_mart_4.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)
I did a cpan -i on XML::Simple and it told me it was up-to-date. I have
connected
to this database (MSD) via Mart before, so I guess the connection params
and the
meta_conf tables should be fine. Any thoughts on why this is not working?
Cheers,
David.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<!--
<MartDBLocation
name = "REACTOME_PATHWAY"
displayName = "REACTOME_PATHWAY"
databaseType = "mysql"
host = "brie8.cshl.edu"
port = "3306"
database = "test_reactome_18_pathway_mart"
schema = "test_reactome_18_pathway_mart"
user = "curator"
password = "Ixact1y"
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
<MartDBLocation
name = "REACTOME_REACTION"
displayName = "REACTOME_REACTION"
databaseType = "mysql"
host = "brie8.cshl.edu"
port = "3306"
database = "test_reactome_18_reaction_mart"
schema = "test_reactome_18_reaction_mart"
user = "curator"
password = "Ixact1y"
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
<MartDBLocation
name = "REACTOME_COMPLEX"
displayName = "REACTOME_COMPLEX"
databaseType = "mysql"
host = "brie8.cshl.edu"
port = "3306"
database = "test_reactome_18_complex_mart"
schema = "test_reactome_18_complex_mart"
user = "curator"
password = "Ixact1y"
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
<MartURLLocation
name = "ensembl"
displayName = "ensembl"
host = "www.biomart.org"
port = "80"
visible = "1"
default = ""
includeDatasets = "hsapiens_gene_ensembl"
martUser = ""
/>
<MartDBLocation
name = "uniprot_mart_17"
displayName = "UniProt"
databaseType = "mysql"
host = "martdb.ebi.ac.uk"
port = "3306"
database = "uniprot_mart_17"
schema = "uniprot_mart_17"
user = "anonymous"
password = ""
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
-->
<MartDBLocation
name = "msd_mart_4"
displayName = "MSD"
databaseType = "mysql"
host = "martdb.ebi.ac.uk"
port = "3306"
database = "msd_mart_4"
schema = "msd_mart_4"
user = "anonymous"
password = ""
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
</MartRegistry>
