Re: [genome-mirror] Rendering species tree with custom genomes

[Stephen Turner]

Thanks for the quick response. 

Christopher: Indeed the dbDbTaxonomy.js file exists, and it's readable by user,group,other. It looks as expected:

turner@ucsc-browser:~$ head -n4 /usr/local/apache/htdocs/js/dbDbTaxonomy.js
/* jshint maxlen: false, unused: false */
var dbDbTree = ["root", 1, null,
[ ["cellular organisms", 131567, null,
  [ ["Eukaryota", 2759, null,
turner@ucsc-browser:~$ wc -l /usr/local/apache/htdocs/js/dbDbTaxonomy.js
1049 /usr/local/apache/htdocs/js/dbDbTaxonomy.js

When I add the line:

hgGateway.dbDbTaxonomy=/usr/local/apache/htdocs/js/dbDbTaxonomy.js

To the end of /usr/local/apache/cgi-bin/hg.conf, I get a 404 in the js console

GET https://cbucsc.formbio.com/usr/local/apache/htdocs/js/dbDbTaxonomy.js net::ERR_ABORTED 404 (Not Found)

Stephen

On Tue, May 21, 2024 at 1:25 PM Christopher Lee <chm...@ucsc.edu> wrote:

Hi Stephen,

Dumb question, but did you make this file:

/usr/local/apache/htdocs/js/dbDbTaxonomy.js

or does it already exist on your server? If you haven't made that yet and you want to add custom genomes to it there are some instructions to create it but I would have to dig them up.

If you already did that and it's not working then we need to see the javascript console.

Thanks,

On Tue, May 21, 2024 at 10:22 AM 'Luis Nassar' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu> wrote:

Hi, Stephen.

There is probably an error message from the javascript on why it failed to load. Could you try reloading that page again with the failed tree and looking to see if there are any errors in the javascript console? Depending on your machine it should be something like Command-Option-J on Mac or ctrl-shift-J on Windows. This should help us diagnose the issue further.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

On Mon, May 20, 2024 at 2:53 PM 'Stephen Turner' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu> wrote:

Hello. I've added custom non-public genomes to a self-hosted mirror, but I can't see them in the species tree. 

When I add the line:

hgGateway.dbDbTaxonomy=/usr/local/apache/htdocs/js/dbDbTaxonomy.js

To the file /usr/local/apache/cgi-bin/hg.conf as suggested in other threads (eg https://groups.google.com/a/soe.ucsc.edu/g/genome-mirror/c/ilXpql3VuWc/m/sLeS6dBnBAAJ), then the tree fails to render altogether. 

I would love further help figuring out how to get my loaded genomes to display in the taxonomy browser. 

Thank you!

Stephen

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending the JavaScript console errors.

The problem is that the hgGateway CGI cannot find your custom dbDbTaxonomy.js file since you defined the absolute path in the hg.conf file:
hgGateway.dbDbTaxonomy=/usr/local/apache/htdocs/js/dbDbTaxonomy.js

The solution is to use a relative path to the dbDbTaxonomy.js file in your hg.conf file:
hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
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Jairo Navarro
UCSC Genome Browser

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[Stephen Turner]

Thanks. That seemed to do the trick. I think the standard taxonomy in dbDbTaxonomy.js may not contain my organisms, or else my organisms in the database lack a taxid, because they're not showing up in the species tree. I'll have to dig a bit more to nail down the root of this problem.

Stephen

[Brandi Cantarel]

Chris, Luis and Jairo,
Could someone point us to the documentation for making that taxonomy js file?  We have some organisms like Asian Elephant and several pigeons that are not in that tree.

[Gerardo Perez]

Hello,

We can point you to our makedoc that has instructions for making the tree: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/dbDbTaxonomy.txt

These instructions with commands were made for internal replication, so you would need to replace hgcentraltest with hgcentral and replace the old date string (set date = 2016_04_18). If you have added genomes to dbDb with dbDb.taxId set to real NCBI Taxonomy IDs, then the instructions should work. Let us know if you encounter any errors and we can help you debug them.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genome Browser

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