Hi Jason,
Here is my registryuRLPointer.xml
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<RegistryURLPointer
name = "central_server"
host = "promoter.dfci.harvard.edu"
port = "80"
path = ""
includeMarts = "msd,uniprot"
/>
</MartRegistry>
Thanks,
Rui
________________________________
From: Jianxin Wang [mailto:[email protected]]
Sent: Wed 10/28/2009 6:40 PM
To: Jing, Rui; [email protected]
Subject: RE: [mart-dev] The problem with Biomart installation - need your help
Hi Jing,
Could you send us your registry.xml file? In your case the
"registryuRLPointer.xml"?
Jason
________________________________________
From: [email protected] [[email protected]] On Behalf Of Jing, Rui
[[email protected]]
Sent: Wednesday, October 28, 2009 4:02 PM
To: [email protected]
Subject: RE: [mart-dev] The problem with Biomart installation - need your help
Hi,
I am trying to install Biomart. When running perl bin/configure.pl -r
conf/registryURLPointer.xml I get the following error message:
Checking prerequisites ...[Looks good]
Use of uninitialized value in string ne at
/home/software/biomart-perl/bin/configureBioMart.pl line 110.
Use of uninitialized value in regexp compilation at
/home/software/biomart-perl/bin/configureBioMart.pl line 112.
rm /home/software/biomart-perl/conf/templates/default/*.ttcrm: cannot remove
`/home/software/biomart-perl/conf/templates/default/*.ttc': No such file or
directory
APACHE: /usr/local/apache/bin/httpd
HOST: promoter
PORT: 80
PROXY:
LOCATION: biomart-perl
APXS/2:
You can change the above configuration by editing
"biomart-perl/conf/settings.conf"
Got usable Apache in /usr/local/apache/bin/httpd, probing for version & ModPerl
configuration
Libdir /home/software/biomart-perl/lib is not in @INC, adding to @INC
Cached Registry Unavailable...
Running Complete Clean...
Problems with the web server: 404 Not Found
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/software/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 254
BioMart::Initializer::_init('BioMart::Initializer=HASH(0xcf381e0)',
'registryFile', '/home/software/biomart-perl/conf/registryURLPointer.xml',
'action', 'cached', 'mode', 'memory') called at
/home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xcf381e0)',
'registryFile', '/home/software/biomart-perl/conf/registryURLPointer.xml',
'action', 'cached', 'mode', 'memory') called at
/home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 328
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xcf381e0)',
'registryFile', '/home/software/biomart-perl/conf/registryURLPointer.xml',
'action', 'cached', 'mode', 'memory') called at
/home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 168
BioMart::Initializer::_new('BioMart::Initializer=HASH(0xcf381e0)',
'registryFile', '/home/software/biomart-perl/conf/registryURLPointer.xml',
'action', 'cached', 'mode', 'memory') called at
/home/software/biomart-perl/bin/../lib/BioMart/RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/software/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached',
'mode', 'memory') called at /home/software/biomart-perl/bin/configureBioMart.pl
line 331
eval {...} at /home/software/biomart-perl/bin/configureBioMart.pl line 330
thanks,
Ray
________________________________
From: [email protected] on behalf of Jing, Rui
Sent: Wed 10/28/2009 2:10 PM
To: [email protected]
Subject: [mart-dev] The problem with Biomart installation - need your help
Hi
I am trying to install Biomart. When running perl bin/configure.pl -r
conf/registryURLPointer.xml I get the following error message:
Checking prerequisites ...[Looks good]
Can't locate XML/Simple.pm in @INC (@INC contains:
/home/software/biomart-perl/bin/../lib
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7
/usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5
/usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7
/usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5
/usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/5.8.8 .) at /home/software/biomart-perl/bin/../lib/BioMart/Web.pm
line 48.
BEGIN failed--compilation aborted at
/home/software/biomart-perl/bin/../lib/BioMart/Web.pm line 48.
Compilation failed in require at (eval 15) line 3.
...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
BEGIN failed--compilation aborted at
/home/software/biomart-perl/bin/../lib/BioMart/Web/TemplateBuilder.pm line 53.
Compilation failed in require at
/home/software/biomart-perl/bin/configureBioMart.pl line 39.
BEGIN failed--compilation aborted at
/home/software/biomart-perl/bin/configureBioMart.pl line 39.
Please would you be able to tell me how to fix this?
Thanks
Ray
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