Customize Taxonomy Tree

[Ho, Eric]

Hi,

I'm trying to configure a GB mirror for a bunch of new species currently not present in UCSC Genome Browser website. I was able to build databases for them but I have encountered difficulty to make the taxonomy tree (on the left of the front page) to reflect only the species available in the database.

Greatly appreciated if someone could give me some ideas.

Eric.

[Eric Ho]

Never mind. I read this document and figured it out.

...../kent/src/hg/makeDb/doc/dbDbTaxonomy.txt

It works.

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[Cath Tyner]

Hi Eric,

I'm glad this is now working for you! 

Here is a similar previously answered question.

I just wanted to include notes about the solution that you already found in case others search the mailing list archives in the future:

First, ensure that all hgcentral.dbDb.taxId values for your new species are valid NCBI Taxonomy IDs:http://www.ncbi.nlm.nih.gov/taxonomy

The tree is generated from dbDb and the NCBI Taxonomy Database as described in kent/src/hg/makeDb/doc/dbDbTaxonomy.txt:

http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/hg/makeDb/doc/dbDbTaxonomy.txt;hb=HEAD

The script kent/src/hg/utils/dbDbTaxonomy.pl is required. You'll need to do a couple things differently from the instructions in dbDbTaxonomy.txt:

use hgcentral instead of hgcentraltest
instead of overwriting ~/kent/src/hg/js/dbDbTaxonomy.js, create a new file in some directory that your CGIs can access.

Then add or change this setting in cgi-bin/hg.conf so that the tree is displayed using your custom file instead of our js/dbDbTaxonomy.js:

# Display phylogenetic tree in hgGateway (URL or path relative to cgi-bin)
hgGateway.dbDbTaxonomy=/path/to/custom/dbDbTaxonomy.js

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Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser