Hi Cynthia, Please check if you have DBI DBD::Oracle installed correctly on your machine. First check if it is installed at all and if so, if it works correctly (you can write a one perl one liner to see if you can connect to the database from the machine that you are running biomart-perl
a On 30/09/10 6:55 PM, "Cynthia Lee" <le...@stanford.edu> wrote: Hello, I'm trying to install BioMart 0.7, but I'm having trouble getting it to configure to my registry file. I created the mart (on oracle) using martbuilder, and am able to open it using mart editor, but when I run the >>perl bin/configure.pl <http://configure.pl> -r conf/biomart.xml command, it keeps giving me the "Problems with the retrieval of dataset configuration" error (pasted below.) I was able to get it running using the sample XML file that came with it (martDBLocation.xml) and when I replace default defaultMartRegistry.xml file in martj0.7, I am able to load it up using martrunner and query around in it just fine... so I don't think the mart is ill-formatted.. Was wondering if someone had any idea as to what's going on, or could offer any insight? here is my registry file: (the host, database and password fields are normally filled in) <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE MartRegistry> <MartRegistry> <virtualSchema name="default"> <MartDBLocation name = "bm" displayName = "biomart" databaseType = "oracle" host = "(host)" port = "1521" database = "(database)" schema = "bm" user = "bm" password = "(password)" visible = "1" default = "" includeDatasets = "" /> </virtualSchema> </MartRegistry> here is the error: [bash $]# perl bin/configure.pl <http://configure.pl> -r conf/biomart.xml Do you want to install in API only mode [y/n] [n]: n Checking prerequisites ...[Looks good] {excerpt} Got usable Apache in /usr/local/apache-2.2.13/bin/httpd, probing for version & ModPerl configuration Have Apache DSO-support and ModPerl library file present, configuring ModPerl in httpd.conf. Libdir /var/www/biomart/lib is not in @INC, adding to @INC Cached Registry Unavailable... Running Complete Clean... Optional setting for martUser in MartDBLocation location:bm not defined - setting to default values !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! COULD NOT CONNECT TO DATABASE bm.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 /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 254 BioMart::Initializer::_init('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 377 BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 328 BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/Initializer.pm line 168 BioMart::Initializer::_new('BioMart::Initializer=HASH(0x12745040)', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/../lib/BioMart/RootI.pm line 64 BioMart::RootI::new('BioMart::Initializer', 'registryFile', '/var/www/biomart/conf/biomart.xml', 'action', 'cached', 'mode', 'memory') called at /var/www/biomart/bin/configureBioMart.pl line 331 eval {...} at /var/www/biomart/bin/configureBioMart.pl line 330 Thanks in advance, Cynthia Lee Arek Kasprzyk Director, Bioinformatics Operations and Principal Investigator Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8559 Toll-free: 1-866-678-6427 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.
