Thanks Richard. Yes, please try this first. If leaving includeDatasets empty in the registry doesn't help, please send me the xml files. Cheers, Junjun
> -----Original Message----- > From: Richard Holland [mailto:[email protected]] > Sent: Thursday, August 13, 2009 1:24 PM > To: Joachim Baran > Cc: Junjun Zhang; [email protected] > Subject: Re: [mart-dev] Creating a single dataset for multiple species > > Each of the new species you added also needs to be added to > the registry XML file you created before they will appear - > my guess is that your current registry only names the first > one you created. Or, you can use the option in the registry > XML to just show all datasets from the mart (if I remember > right this is by leaving includeDatasets as a blank value). > > cheers, > Richard > > On 13 Aug 2009, at 17:55, Joachim Baran wrote: > > > Hello, > > > > 2009/7/20 Junjun Zhang <[email protected]>: > >> As Syed pointed out earlier on, you start with one species by run > >> Naïve and Export the naïve configure to the database, and then > >> "Alt-N" to bring in the other species. When prompted with the > >> question "Create new template rather than use existing one?", ask > >> "No". After this, a template configure will be created. When you > >> expend the "PartitionTable: Datasets" > >> node in the left tree panel, you should be able to see two > >> "Partition", one for each species. Don't forget to do > "Export" again. > >> From now on, you should be able to make changes to the > configuration, > >> and the changes will be propagate to the two species. > >> Follow the same process to add more species as you need. > > Adding the species worked fine and I do indeed see several > datasets in > > the tree on the left-hand side in MartEditor now. However, after > > exporting and running 'perl bin/configure.pl --clean -r > > conf/myMart.xml' again, I do not see the added species in the > > selection box '- CHOOSE DATASET -' in the BioMart > web-interface. The > > selection box only contains the choice 'my ensembl', which > corresponds > > to the name that I have chosen for the template in MartEditor. In > > fact, when I choose this entry, the data I can query seems to > > correspond to the first species for which I have run 'Naive' in > > MartEditor first. > > > > How do I make the other species appear in that selection > box as well? > > > > Thanks, > > Joachim > > > > -- > > B.1079 Michael Smith Building > > Faculty of Life Sciences > > The University of Manchester > > Oxford Road > > Manchester > > M13 9PT > > United Kingdom > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: [email protected] > http://www.eaglegenomics.com/ > >
