Hi Alexie
Try this
<virtualSchema name="default" visible="1" default="1">
instead of
<virtualSchema name="default">
Good Luck!
Cheers
Syed
> hello again
> seen this?
> ERROR something wrong with your registry:
> Initializer.pm: Set at least one virtaulSchema attribute
> default="1"
>
> following the user guide my test registry look like this:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
> <virtualSchema name="default">
> <MartDBLocation
> name = "ent-lit"
> displayName = "Entomology Literature"
> databaseType = "postgres"
> host = "localhost"
> port = "3306"
> database = "ent-lit"
> schema = "ent_lit_mart"
> user = "alexie"
> password = ""
> visible = "1"
> default = ""
> includeDatasets = ""
> />
> </virtualSchema>
> </MartRegistry>
>
> is there something missing? Proceeding blindly, I tried default="1" or
> default="true" but that didn't change the error message. The trace
> message follows below.
> Please note that this is not the first register i load to BioMart. but I
> scrolled up in the instructions and it only informs of two options: a
> renamed file (the command i use) and the one with the clean option.
>
> ta
> alexie
>
>
> ERROR something wrong with your registry:
> Initializer.pm: Set at least one virtaulSchema attribute
> default="1"
> Trace begun at
> /usr/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 686
> BioMart::Initializer::_loadConfigFrom('BioMart::Initializer=HASH(0x21007e0)',
> 'IO::File=GLOB(0x21004f0)') called at
> /usr/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 240
> BioMart::Initializer::_init('BioMart::Initializer=HASH(0x21007e0)',
> 'registryFile', '/usr/software/biomart-perl/conf/myRegistry.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /usr/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393
> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x21007e0)',
> 'registryFile', '/usr/software/biomart-perl/conf/myRegistry.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /usr/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 344
> BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x21007e0)',
> 'registryFile', '/usr/software/biomart-perl/conf/myRegistry.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /usr/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 184
> BioMart::Initializer::_new('BioMart::Initializer=HASH(0x21007e0)',
> 'registryFile', '/usr/software/biomart-perl/conf/myRegistry.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /usr/software/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
> '/usr/software/biomart-perl/conf/myRegistry.xml', 'action', 'cached',
> 'mode', 'memory') called at
> /usr/software/biomart-perl/bin/configureBioMart.pl line 339
> eval {...} at /usr/software/biomart-perl/bin/configureBioMart.pl line 338
>
>
> I also tried to re-configure using the test registryURLPointer.xml but I
> got this error (with --update or --clean commands...)
>
> ERROR something wrong with your registry:
> syntax error at line 1, column 0, byte 0 at
> /usr/lib/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi/XML/Parser.pm
> line 187
>
> --
> Alexie Papanicolaou
>
> Entomology
> Max Planck Institute for Chemical Ecology
> Hans Knoell Str 8
> 07745 Jena
> Germany
>
> [EMAIL PROTECTED]
>
>
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
