Hi Glen,
Sounds like the cached registry object never got created from your configure.pl. What do you get if you ls -l conf/cachedRegistries?
BTW are you planning on setting up an interesting BioMart at JAX. I am currently building a mouse resource portal here at the EBI using BioMart underneath so feel free if you need support from me.
Best wishes, Damian On Tue, 7 Oct 2008, Glen Beane wrote:
I am trying to setup biomart-perl on OS X 10.5. I am using the stock apache2, and have installed mod_perl from source. I am able to load mod_perl after modifying the standard apache2 .conf file. I have installed all the prerequisite perl modules for biomart, and have run perl bin/configure.pl -r conf/registryURLPointer.xml For now I am just testing biomart, so the biomart-perl folder is on my desktop Then I start up apache: /usr/sbin/httpd -d /Users/gbeane/Desktop/biomart-perl/ -f /Users/gbeane/Desktop/biomart-perl/conf/httpd.conf Processing Cached Registry: /Users/gbeane/Desktop/biomart-perl/conf/cachedRegistries/registryURLPointer. xml.cached Syntax error on line 44 of /Users/gbeane/Desktop/biomart-perl/conf/httpd.conf: Can't call method "settingsParams" on an undefined value at /Users/gbeane/Desktop/biomart-perl/lib/BioMart/Initializer.pm line 623.\n Can someone point me in the right direction to diagnose this error? Here is the output from when I run the bin/configure.pl script: perl bin/configure.pl -r conf/registryURLPointer.xml --clean Do you want to install in API only mode [y/n] [n]: Checking prerequisites ...[Looks good] Subroutine BioMart::Web::Zlib::adler32 redefined at /System/Library/Perl/5.8.8/Exporter.pm line 65. at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 Subroutine BioMart::Web::Zlib::crc32 redefined at /System/Library/Perl/5.8.8/Exporter.pm line 65. at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 Subroutine BioMart::Web::Zlib::ZLIB_VERNUM redefined at /System/Library/Perl/5.8.8/Exporter.pm line 65. at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 Subroutine BioMart::Web::Zlib::MAX_MEM_LEVEL redefined at /System/Library/Perl/5.8.8/Exporter.pm line 65. at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 Subroutine BioMart::Web::Zlib::MAX_WBITS redefined at /System/Library/Perl/5.8.8/Exporter.pm line 65. at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 Subroutine BioMart::Web::Zlib::Z_DEFAULT_COMPRESSION redefined at /System/Library/Perl/5.8.8/Exporter.pm line 65. at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 Subroutine BioMart::Web::Zlib::Z_DEFAULT_STRATEGY redefined at /System/Library/Perl/5.8.8/Exporter.pm line 65. at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 Subroutine BioMart::Web::Zlib::Z_DEFLATED redefined at /System/Library/Perl/5.8.8/Exporter.pm line 65. at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 APACHE: /usr/sbin/httpd HOST: test.biomart.org PORT: 9002 PROXY: LOCATION: biomart APXS/2: You can change the above configuration by editing "biomart-perl/conf/settings.conf" Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl configuration Have Apache DSO-support and ModPerl library file present, configuring ModPerl in httpd.conf. Libdir /Users/gbeane/Desktop/biomart-perl/lib is not in @INC, adding to @INC Connection parameters of [MSD PROTOTYPE (EBI UK)] [ OK ] Connection parameters of [UNIPROT PROTOTYPE (EBI UK)] [ OK ] [NEW CONFIGURATION] .... WITH MEMORY [default] default ... MSD PROTOTYPE (EBI UK) ... 001/001 ... msd ....................................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6/0.7 ... OK default ... UNIPROT PROTOTYPE (EBI UK) ... 001/006 ... uniprot_location .......................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6/0.7 ... OK default ... UNIPROT PROTOTYPE (EBI UK) ... 002/006 ... uniprot_sequence .......................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6/0.7 ... OK default ... UNIPROT PROTOTYPE (EBI UK) ... 003/006 ... uniprot_cell_component .................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6/0.7 ... OK default ... UNIPROT PROTOTYPE (EBI UK) ... 004/006 ... uniprot_biol_process ...................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6/0.7 ... OK default ... UNIPROT PROTOTYPE (EBI UK) ... 005/006 ... uniprot ................................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6/0.7 ... OK default ... UNIPROT PROTOTYPE (EBI UK) ... 006/006 ... uniprot_mol_function ...................... (WEB) www.biomart.org:80 ............ -> upgrading to 0.6/0.7 ... OK Setting possible links between datasets ....(scanning) 100% ....(linking) 100% ....(sorting) 100% ....(clustering) 7/7 ....(resolving) 100% Building templates for visible datasets .... 100% Compiling templates for visible datasets [1/2] Attribute Panel of Dataset.. :msd [1/2] Filter Panel of Dataset..... :msd [2/2] Attribute Panel of Dataset.. :uniprot [2/2] Filter Panel of Dataset..... :uniprot -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153
