Hello,
I am trying to install Biomart on a Ubuntu based system. I have
installed Apache, Mod_Perl and When I trying to configure MartView
with the registryURL file(attached), I am getting error (Attached).
I am not sure where the error is. Could you help me pointing out where
the error is?
Thanks and regards,
Sri Krishna
Do you want to install in API only mode [y/n] [n]:
Checking prerequisites ...[Looks good]
APACHE: /home/ssri/biomart/apache/bin/httpd
HOST: localhost
PORT: 9002
PROXY:
LOCATION: biomart
APXS/2:
You can change the above configuration by editing "biomart-perl/conf/settings.conf"
Got usable Apache in /home/ssri/biomart/apache/bin/httpd, probing for version & ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring ModPerl in httpd.conf.
Libdir /home/ssri/biomart/biomart-perl/lib is not in @INC, adding to @INC
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)
Trace begun at /home/ssri/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm line 254
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x2a0c068)', 'registryFile', '/home/ssri/biomart/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached', 'mode', 'memory') called at /home/ssri/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x2a0c068)', 'registryFile', '/home/ssri/biomart/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached', 'mode', 'memory') called at /home/ssri/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm line 328
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x2a0c068)', 'registryFile', '/home/ssri/biomart/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached', 'mode', 'memory') called at /home/ssri/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm line 168
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x2a0c068)', 'registryFile', '/home/ssri/biomart/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached', 'mode', 'memory') called at /home/ssri/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile', '/home/ssri/biomart/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached', 'mode', 'memory') called at /home/ssri/biomart/biomart-perl/bin/configureBioMart.pl line 332
eval {...} at /home/ssri/biomart/biomart-perl/bin/configureBioMart.pl line 331
Cached Registry Unavailable...
Running Complete Clean...
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<RegistryURLPointer
name = "central_server"
host = "www.biomart.org"
port = "80"
path = ""
includeMarts = "msd,uniprot"
/>
</MartRegistry>
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