On 19 Dec 2006, at 16:57, Marina Olhovsky wrote:
Hi Marina,
could you re-post your mail again to the list making sure
it is in plain text please? we'll then be able to help you
a.
Hi Arek,
I've set up my own mart, and now I wish to launch Martview to do a
search. I created a configuration file myRegistry.xml that looks like
this:
<MartRegistry>
<virtualSchema name="default">
<MartDBLocation
name="test_mart"
displayName="My Mart"
databaseType="postgresql"
host="localhost"
database="test_mart"
port="5432"
schema="test_mart"
user="my_user"
password="my_passwd"
visible="1"
default="1"
includeDatasets=""
/>
</virtualSchema>
</MartRegistry>
From my_biomart dir execute:
sudo perl bin/configure.pl -r conf/myRegistry.xml
Do you want to install in API only mode [y/n] [n]: n
Checking prerequisites ...[Looks good]
DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]: n
Checking several common Apache locations...done.
Select either one of the detected httpd paths on the list, OR enter
the path you wish to use:
/usr/sbin/httpd2
[1]:
Got usable Apache in /usr/sbin/httpd2, probing for version & ModPerl
configuration
Have Apache DSO-support and ModPerl library file present, configuring
ModPerl in httpd.conf.
Enter the server host OR default [your_server]:
Enter the server port OR default [5555]:
Enter proxy OR default :
Enter the required script location OR default [biomart]:
Libdir /home/olhovsky/biomart-perl/lib is not in @INC, adding to @INC
Cached Registry Unavailable...
Running Complete Clean...
ERROR something wrong with your registry:
Initializer.pm: Set at least one virtaulSchema
attribute default="1"
Trace begun at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line 686
BioMart::Initializer::_loadConfigFrom('BioMart::
Initializer=HASH(0x939810c)', 'IO::File=GLOB(0x939876c)') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line 240
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x939810c)',
'registryFile', '/home/olhovsky/biomart-perl/conf/myRegistry.xml',
'action', 'cached', 'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393
Hi Marina,
in your registry file try
<virtualSchema name="default" visible="0" default="1">
instead of
<virtualSchema name="default">
and see if this helps
a.
BioMart::Initializer::init_clean('BioMart::
Initializer=HASH(0x939810c)', 'registryFile',
'/home/olhovsky/biomart-perl/conf/myRegistry.xml', 'action', 'cached',
'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line 344
BioMart::Initializer::init_cached('BioMart::
Initializer=HASH(0x939810c)', 'registryFile',
'/home/olhovsky/biomart-perl/conf/myRegistry.xml', 'action', 'cached',
'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/Initializer.pm line 184
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x939810c)',
'registryFile', '/home/olhovsky/biomart-perl/conf/myRegistry.xml',
'action', 'cached', 'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/olhovsky/biomart-perl/conf/myRegistry.xml', 'action', 'cached',
'mode', 'memory') called at
/home/olhovsky/biomart-perl/bin/configureBioMart.pl line 339
eval {...} at /home/olhovsky/biomart-perl/bin/configureBioMart.pl
line 338
------------------------------------------------------------------------
-------
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
------------------------------------------------------------------------
-------
