feature request

[jp d]

hi,
any chance you could put the clade and genome pull down
options thing back in the hgGateway page ?
something like these images
http://bergmanlab.ls.manchester.ac.uk/wordpress/wp-content/uploads/2012/03/output.png

we have a mirror with species that you dont have and i can't seem to find
a way to change the genome to (for example) other species of yeast
from the gateway page.
i tried sending it species and taxId arguments to hgGateway but no luck

as a workaround, i can send it to other genomes with a db=whatever argument to hgTracks
but i can't figure out how to see it from the gateway page

or any suggestions would be appreciated

thanks
jpd

[Angie Hinrichs]

Hi jpd,

Sorry to hear that the redesign makes it less convenient to access your added species.  Have you tried searching for those species in the text search box on the left that says "Enter species or common name"?  It should search your local hgcentral.dbDb table (fields: name, genome, scientificName) so it should be able to match the added species.  

If your added species have valid NCBI Taxonomy identifiers in hgcentral.dbDb.taxId, with a one-to-one correspondence with their names in dbDb.genome, then you can build a custom phylogenetic tree that includes your species.  The method is described here: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/makeDb/doc/dbDbTaxonomy.txt;hb=HEAD

You will need to substitute some local directory names, and "hgcentral" for "hgcentraltest".  Instead of placing the resulting dbDbTaxonomy.js file in ~/kent/src/hg/js/dbDbTaxonomy.js, I recommend giving it a new name, for example dbDbTaxonomy.bergmanlab.js.  

You will also need the perl script kent/src/hg/utils/dbDbTaxonomy.pl (http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/utils/dbDbTaxonomy.pl;hb=HEAD).  

If you name the new file dbDbTaxonomy.bergmanlab.js then you will need to copy it into the web server directory htdocs/js/ and add this line to the web server cgi-bin/hg.conf file:

hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.bergmanlab.js

I hope that helps, and please send any questions to genome...@soe.ucsc.edu.  

Angie

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