On Thu, 2007-02-08 at 11:55 +0200, Etai Jacob wrote: Hi Etai
> Hi, > I have installed biomart and did the following before executing martview: > > 1) Define your mart in MartBuilder > 2) Use MartBuilder to generate SQL that will create the mart out of your > source data. Run that SQL. > 3) Connect to the created mart using MartEditor and configure the > attributes and filters you want (the Naive option will do this for you > with sensible defaults) > 4) Export the config from MartEditor so that it is saved in your mart > 5) Create a registry XML file that describes how to find your newly > configured mart > 6) Run bin/configure.pl using the registry XML and --clean Looks as if your registry is not getting configured properly. Could be due to incorrect xmls representing your marts (I am not talking about registry.xml file). Could you please have a look at the on-screen messages while you are configuring your martview and see if there is somehting wrong there. Might help us understanding your problem in a better way. Kind regards Syed > 7) Start up MartView > > as described in [[mart-dev] martview problems, Jennifer Siepen] > > The registry.xml file: > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE MartRegistry> > <MartRegistry> > <virtualSchema name="default" visible="1" default="1"> > <MartDBLocation > name = "DGV" > displayName = "DGV" > databaseType = "mysql" > host = "dell7" > port = "3306" > database = "DGV" > schema = "DGV" > user = "****" > password = "****" > visible = "1" > default = "" > includeDatasets = "" > /> > </virtualSchema> > </MartRegistry> > > I keep getting the error (web): > > ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method > "settingsParams" on an undefined value at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web.pm line 116. > > If you repeatedly get directed to this error page, there may be a > problem with your current session parameters. To clear your session > and start with a clean slate, please click the button below. > > Stacktrace: > Exception::Class::Base::new > /home/etai/.html/biomart/biomart-perl/cgi-bin/martview.cgi:80 > > Running the martview from command line results with the same error. > I followed each step as described in ([mart-dev] martview problems, > Jennifer Siepen) but I am still getting the same error. > > Any suggestions are happily welcome. > > Thanks, > Etai -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
