On 19 Jan 2007, at 17:06, David Croft wrote:
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?
Hi David,
I just copied and pasted our registry and run it with the latest 0.5.
It works fine. You probably are running it from some place that you
cannot
see martdb.
Can you do the following little test to see if can connect to martdb:
bigmac: ~[arek] telnet martdb.ebi.ac.uk 3306
Trying 193.62.197.154...
Connected to martdb.ebi.ac.uk.
Escape character is '^]'.
4
4.0.17-standard-log?8EeN6`cPH,Connection closed by foreign host.
cheers,
a.
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>
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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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