Hi Syed, I would like to use the combination of BioMart / ProServer / GBrowse to maintain and visualize genomic assemblies and maybe more data later on.
To understand how to setup BioMart / ProServer I'm using the dataset included in http://gmod.org/wiki/BioMart_Tutorial With MartEditor I created an importable/exportable pair with internalName, displayName, linkName and name set to "mypair". I set the "type" field to "dasGene" for both. For importable I set the filters field to "stable_id_1023" and for exportable, I set the attributes to "stable_id_1023,seq_region_start_1020,seq_region_end_1020,biotype_1020,source_1018". For the ProServer configuration, I set: feature_keys = id,start,end,type,method Calling ProServer from a webbrowser causes an error: Use of uninitialized value $call in string eq at blib/lib/Bio/Das/ProServer.pm line 859. Connection parameters of [My BioMart Database] [ OK ] default ... My BioMart Database ...... 001/001 ... mydemo .................................... (RDBMS) localhost:3306 ................ OK Setting possible links between datasets ....(scanning) 100% ....(linking) 100% ....(sorting) 100% ....(clustering) 1/1 - 0 remain ....(resolving) 100% Error building adaptor 'Bio::Das::ProServer::SourceAdaptor::biomart' for 'mymart1': Can't call method "getImportables" on an undefined value at /usr/local/share/perl/5.10.0/Bio/Das/ProServer/SourceAdaptor/biomart.pm line 84. at blib/lib/Bio/Das/ProServer.pm line 794 Okay, this is not an BioMart specific, but maybe someone has a clue what's going on. Cheers, Charles
