63c0f6234dbcc0c3fdc9bc2d0e673c8313bd6443 mspeir Sun Sep 27 11:57:25 2026 -0700 two minor fixes from automated CR, #37641 diff --git src/hg/htdocs/goldenPath/help/assemblyHubHelp.html src/hg/htdocs/goldenPath/help/assemblyHubHelp.html index d854232b295..5444e08261a 100755 --- src/hg/htdocs/goldenPath/help/assemblyHubHelp.html +++ src/hg/htdocs/goldenPath/help/assemblyHubHelp.html @@ -416,31 +416,31 @@ longLabel Variant calls over hg19 region type vcfTabix visibility pack bigDataUrl http://myServer.com/data/example.vcf.gz

If your hub requires a reference genome sequence, you can still provide a .2bit file with twoBitPath. Grouping (previously in -groups.txt). can also be integrated here if needed. +groups.txt) can also be integrated here if needed.

Once hosted on a server, the single configuration file (and associated data files such as .bigWig, .vcf.gz, .2bit) can be loaded into the UCSC Genome Browser via the Connected Hubs tab of the Track Data Hubs page.

Building Tracks

Tracks are defined in the trackDb.txt file, where each stanza specifies how tracks are displayed (shortLabel, longLabel, color, visibility), along with other information such as the group the track belongs to (referencing groups.txt) and whether additional HTML should be displayed when a user clicks into the track or a track item:

@@ -770,31 +770,30 @@
 		IP/port configuration is incorrect.
The genomes.txt file should also be checked to confirm that the BLAT line matches the correct IP and port. For example:
blat 132.249.245.79 17777
Instead of:
blat localhost 17777
  • Check gfServer status
    Request status directly from gfServer:
    gfServer status yourLocation yourPort
    For example:
    gfServer status 132.249.245.79 17777
    Sample output might look like:
     version 39x1
     serverType static
    -version 39x1
     type nucleotide
     host localhost
     port 17777
     tileSize 11
     stepSize 5
     minMatch 2
     pcr requests 0
     blat requests 0
     bases 0
     misses 0
     noSig 0
     trimmed 0
     warnings 0
     
  • Test with gfClient