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Opening track hubs by URL

TL;DR: The &hubURL= query parameter opens a UCSC track hub straight from a link, with no config file to set up first. Whoever opens the link lands in JBrowse with the hub's assemblies and tracks already available.

Basic usage

https://jbrowse.org/code/jb2/latest/?config=none&hubURL=https://example.com/hub.txt
  • hubURL= points directly at the hub's hub.txt file (the same URL you would paste into the connection form).
  • config=none skips loading a JBrowse config, because the hub supplies its own assemblies and tracks. See ?config=.

JBrowse reads the hub's shortLabel and uses it as the session name.

Combining with a config

Drop config=none and point ?config= at a real config when the launch needs something the hub does not carry, such as plugins or extra assemblies:

?config=myconfig.json&hubURL=https://example.com/hub.txt

The hub's tracks are added on top of whatever the config already defines.

Opening the hub at a specific location

By default a hub opens wherever it says to (defaultPos in its genomes stanza). Add &loc= and &assembly= to land somewhere else:

?config=none&hubURL=https://example.com/hub.txt&assembly=GCF_019202715.1&loc=chr1:1-100000

&assembly= is required here, and it is the hub's genome ID — the same name the hub's genomes.txt (or its genome line, for a one-file hub) uses. &loc= on its own has no assembly to resolve against, so JBrowse loads the hub at its own default location and says why. &tracks= works the same way, naming track IDs the hub defines.

Loading several hubs

Pass a comma-separated list to open more than one hub at once:

?config=none&hubURL=https://example.com/hubA.txt,https://example.com/hubB.txt

Each hub becomes its own category in the track selector.

How a loaded hub behaves

Each hub URL becomes a UCSC track hub connection in the session, and from there it behaves exactly like a connection you added by hand: lazily loaded, its own category in the track selector, and only the tracks you open stored in the session.

Hub tracks match to assemblies by genome ID, and the assemblies available are whatever the hub carries plus whatever a combined ?config= defines, so a hub opened with config=none shows only the tracks its own assemblies cover.

See also