Hello Again,
I cannot figure out what the problem could be when trying to connect to my
newly created mart. I am using the exact parameters in my registry .xml file
that I am using to connect via MartBuilder and MartEditor. I've attached the
stack trace I am getting when trying to run configure.pl.
Any help would make me so happy.
Thanks again All!
j...@jars-desktop:~/biomart/biomart-perl$ sudo perl bin/configure.pl -r
conf/NUgeneRegistry.xml
Do you want to install in API only mode [y/n] [n]:
Checking prerequisites ...[Looks good]
APACHE: /usr/sbin/apache2
HOST: test.biomart.org
PORT: 9002
PROXY:
LOCATION: biomart
APXS/2: /usr/bin/apxs2
You can change the above configuration by editing
"biomart-perl/conf/settings.conf"
Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl
configuration
Have Apache DSO-support and ModPerl library file present, configuring ModPerl
in httpd.conf.
Libdir /home/jars/biomart/biomart-perl/lib is not in @INC, adding to @INC
Cached Registry Unavailable...
Running Complete Clean...
Optional setting for martUser in MartDBLocation location:CGM_NUGENE_BIOMART not
defined - setting to default values
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
COULD NOT CONNECT TO DATABASE XE.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)
Trace begun at
/home/jars/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm line 254
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x9432a30)',
'registryFile', '/home/jars/biomart/biomart-perl/conf/NUgeneRegistry.xml',
'action', 'cached', 'mode', 'memory') called at
/home/jars/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x9432a30)',
'registryFile', '/home/jars/biomart/biomart-perl/conf/NUgeneRegistry.xml',
'action', 'cached', 'mode', 'memory') called at
/home/jars/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm line 328
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x9432a30)',
'registryFile', '/home/jars/biomart/biomart-perl/conf/NUgeneRegistry.xml',
'action', 'cached', 'mode', 'memory') called at
/home/jars/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm line 168
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x9432a30)',
'registryFile', '/home/jars/biomart/biomart-perl/conf/NUgeneRegistry.xml',
'action', 'cached', 'mode', 'memory') called at
/home/jars/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/jars/biomart/biomart-perl/conf/NUgeneRegistry.xml', 'action', 'cached',
'mode', 'memory') called at
/home/jars/biomart/biomart-perl/bin/configureBioMart.pl line 331
eval {...} at /home/jars/biomart/biomart-perl/bin/configureBioMart.pl line 330
