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/
