On 12 Jun 2007, at 11:53, Syed Haider wrote:
Hi Brian
This is fixed now and will be a part of our about to be released
biomart-perl 0.6.
Thanks for spotting.
meanwhile it should still work if you remove the virtual schema tag
a.
Cheers
Syed
Begin forwarded message:
From: Brian Osborne <[EMAIL PROTECTED]>
Date: 11 June 2007 20:29:32 BST
To: "[email protected]" <[email protected]>
Subject: [mart-dev] Initializer error
mart-dev,
I'm setting up MartView to connect to a local mart constructed with
MartBuilder. I create myRegistry.xml as suggested on page 18 of the
manual,
it looks like this:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<virtualSchema name="testmart1">
<MartDBLocation
name = "testmart1"
displayName = "testmart1"
databaseType = "postgres"
host = "localhost"
port = "5432"
database = "bioseqdb"
schema = "biosql"
user = "postgres"
password = ""
visible = "1"
default = "1"
includeDatasets = ""
martUser = ""
includeMarts = ""
/>
</virtualSchema>
</MartRegistry>
Now the next step is not clear but I assume you're supposed to run
configure.pl:
282 ~/biomart-perl>perl bin/configure.pl -r conf/myRegistry.xml
But I see an error:
Do you want to install in API only mode [y/n] [n]:
Checking prerequisites ...[Looks good]
DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]:
Cached Registry Unavailable...
Running Complete Clean...
ERROR something wrong with your registry:
Initializer.pm: Set at least one virtaulSchema
attribute
default="1"
How do I fix this?
Thanks again,
Brian O.
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
------------------------------------------------------------------------
-------
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
------------------------------------------------------------------------
-------
