Hi Junjun,
The same problem when I ran: perl bin/configure.pl -r conf/martDBLocation.xml.
Please let me know what the problem is. do I need to change martDBLocation.xml?
Thanks,
the content of my conf files:
1. martDBLocation.xml
<MartRegistry>
<MartDBLocation
name = "msd_mart_4"
displayName = "My BioMart Database"
databaseType = "mysql"
host = "martdb.ebi.ac.uk"
port = "3306"
database = "msd_mart_4"
schema = "msd_mart_4"
user = "anonymous"
password = ""
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
</MartRegistry>
2. settings.conf
[httpdSettings]
apacheBinary=/usr/local/apache/bin/httpd
serverHost=promoter.dfci.harvard.edu
port=80
# to use proxying set the proxy port below (even if its 80) and set serverHost
as your proxy host
proxy=
# if apxs or apxs2 is not in default directory where httpd lives, you may set
this param to point to apxs/2
apxs=
location=biomart-perl
[r...@promoter biomart-perl]# perl bin/configure.pl -r conf/martDBLocation.xml
Do you want to install in API only mode [y/n] [n]:
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.dfci.harvard.edu
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...
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
COULD NOT CONNECT TO DATABASE msd_mart_4.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/software/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 254
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x15eb8150)',
'registryFile', '/home/software/biomart-perl/conf/martDBLocation.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(0x15eb8150)',
'registryFile', '/home/software/biomart-perl/conf/martDBLocation.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(0x15eb8150)',
'registryFile', '/home/software/biomart-perl/conf/martDBLocation.xml', 'action',
'cached', 'mode', 'memory') called at
/home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 168
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x15eb8150)',
'registryFile', '/home/software/biomart-perl/conf/martDBLocation.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/martDBLocation.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: Junjun Zhang [mailto:[email protected]]
Sent: Thu 10/29/2009 10:47 AM
To: Jing, Rui; Jianxin Wang; [email protected]
Subject: RE: [mart-dev] The problem with Biomart installation - need your help
Hi Ray,
Thanks for sending us the registry.
Since you are first time biomart user, I do not encourage you use
'RegistryURLPointer' in your registry file. Rather, please use one of the
registry examples under 'conf' directory, for example, martDBLocation.xml. After
you run bin/configure.pl with this registry file successfully, then you know the
installation is OK.
Let us know how it goes.
Kind regards,
Junjun
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of Jing, Rui
> Sent: Thursday, October 29, 2009 9:46 AM
> To: Jianxin Wang; [email protected]
> Subject: RE: [mart-dev] The problem with Biomart installation
> - need your help
>
> 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(0x
> cf381e0)',
> '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(0
> xcf381e0)',
> '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/TemplateBui
> lder.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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