faffaf6750cf5492f3bd779a8e2d3fe4116e24d6 jnavarr5 Tue Jul 28 14:53:49 2026 -0700 Documenting the codonTable genomes.txt setting on the trackDb hub settings page and the track hub help page, with the changes page now linking to the new settings entry, refs #16550 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 21ad504243e..bf1f741f3a0 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -700,30 +700,36 @@ organism - the string which is displayed along with the description on most title pages in the Genome Browser. Adjust your names in organism and description until they are appropriate. This organism name is the name that appears in the genome pull-down menu on the browser gateway page.

scientificName - specifies the scientific name for the assembly.

defaultPos - specifies the default position the genome browser will open when a user first views this assembly. This is usually selected to highlight a popular gene or region of interest in the genome assembly.

orderKey - used with other genome definitions at this hub to order the genome pull-down.

htmlPath - refers to an html file that is used on the gateway page to display information for a novel assembly.

+codonTable - an optional setting that assigns +NCBI genetic +codes (codon translation tables) to individual sequences for amino acid display, for example +codonTable default=1 NC_017929.1=13; see the assembly hub +codonTable documentation for details.

Example genomes.txt including a newOrg1 assembly

genome hg18
 trackDb hg18/trackDb.txt
 

 genome hg19
 trackDb hg19/trackDb.txt
 

 genome newOrg1
 trackDb newOrg1/trackDb.txt
 twoBitPath newOrg1/newOrg1.2bit
 groups newOrg1/groups.txt
 description Big Foot V4
 organism BigFoot
 defaultPos chr21:33031596-33033258
 orderKey 4800