Hi Berenice,
Glad that you have solved the problem with missing DBD module. With the message
you sent to us below, it seemed configure.pl had run successfully with
martDBLocation.xml registry file. I am wondering after the configuration if
you've even tried starting apache server and checking the martview from your
web browser. If you did try, how was it?
As for the registryURLPointer.xml file, it is intended for other people to use
to include your datamart as part of their mart federation (of course you must
expose your mart to them first). For your self-made mart, martDBLocation.xml is
the only choice to bring your datamart online. registryURLPointer.xml (as you
showed below) will NOT work, just as the name suggested, it's a pointer
pointing to a running BioMart server instance (which has to be configured using
martDBLocation in the first place), in other words, registryURLPointer can not
be used to configure a first-hand (ie, self-made) datamart.
If you really want to try out a registryURLPointer file, try this one:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<RegistryURLPointer
name = "central_server"
host = "www.biomart.org"
port = "80"
path = ""
includeMarts = "ensembl,sequence"
/>
</MartRegistry>
This will work, because there is a running biomart server (www.biomart.org)
which will provide you services including full configuration of the marts you
are going to include in your mart federation.
Hope this helps a bit.
Junjun
--------------------------------------------------------------------------------
From: [email protected] [mailto:[email protected]] On Behalf Of
[email protected]
Sent: Monday, February 23, 2009 9:06 AM
To: Syed Haider
Cc: [email protected]; [email protected]; Syed Haider
Subject: Re: [mart-dev] Error Stating MartView
Hi,
I corrected the error of connection. In fact there was a missing perl library
DBD.
Now, When, I launch the command perl bin/configure.pl -r
conf/martDBLocation.xml --clean
The trace is :
Connection parameters of [Testsysbio] [ OK ]
[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... Testsysbio ............... 001/001 ... AraGene
................................... (RDBMS) XXXXXXXXXXXXX:3306 . OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 1/1 - 0 remain
....(resolving) 100%
Building templates for visible datasets
.... 100%
Compiling templates for visible datasets
[1/1] Attribute Panel of Dataset.. :AraGene
[1/1] Filter Panel of Dataset..... :AraGene
But when I lauch the command perl bin/configure.pl -r
conf/registryURLPointer.xml
I have reconfigure a little the registryURLPointer.xml
</MartRegistry>
This is my RegistryDBPointer.xml, I added here my own mart.
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE MartRegistry (View Source for full doctype...)>
<MartRegistry>
<RegistryDBPointer name="Testsysbio" host="XXXXXX" port="3306"
user="XXXXX" password="XXXXXX" database="Testsysbio" schema="
Testsysbio" databaseType="mysql" includeMarts="AraGene" />
</MartRegistry>
there is still an error.
Checking prerequisites ...[Looks good]
rm /home/cropdesign/biomart/biomart-perl/conf/templates/default/*.ttc
APACHE: /usr/sbin/apache2
HOST: localhost
PORT: 80
PROXY:
LOCATION: /home/cropdesign/biomart/biomart-perl
APXS/2:
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/cropdesign/biomart/biomart-perl/lib is not in @INC, adding
to @INC
Cached Registry Unavailable...
Running Complete Clean...
ERROR something wrong with your registry:
syntax error at line 1, column 0, byte 0 at
/usr/lib/perl5/XML/Parser.pm line 187
Do you have an idea on my error?
Best regards,
Thanks,
Bérénice
Berenice Wulbrecht
Phone: +32 9 242 9172, E-Mail: [email protected]
Postal Address: CropDesign N.V., - - CD2, 9052 Gent (Zwijnaarde), Belgium
CropDesign N.V. - A BASF Plant Science Company
CropDesign N.V.
Technologiepark 3
B-9052 Gent
Belgium
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