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Plugin store

TL;DR: The in-app plugin store lets you browse, search, and install community plugins into the current session. Plugins can add new track types, view types, data adapters, and custom menu items, and some carry their own data with them.

The full catalog of white-listed plugins, each with its config snippet, is also listed on the plugin store page.

To write your own plugin, see the developer guide.

Where the install persists depends on the context:

  • web session - saved into the session and travels with the share link
  • admin server - written to config.json, persists across sessions
  • JBrowse Desktop - saved into the open session file

Some plugins (e.g. CIVIC) add their data automatically when installed. Others only register building blocks (a new track type, a new adapter) that need a matching config entry to be useful. Ask an admin if you can't edit the config yourself.

The plugin store inside the app. Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses volvox, loaded from a .2bit genome.
  2. Type your region of interest into the location box and press Enter.This figure is at ctgA:1-20000.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=test_data%2Fvolvox%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22volvox%22%2C%22loc%22%3A%22ctgA%3A1-20000%22%7D%5D%7D&sessionName=JBrowse+docs%3A+plugin_store

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:1-20000"
    }
  ]
}

Loaded against config: test_data/volvox/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("volvox", "https://your-server/your-genome.fa.gz"),
    location="ctgA:1-20000",
)

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:1-20000"
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/volvox/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Keeping a plugin for every visit

A plugin installed in a web session goes when the session does: a new session, or someone else's link, starts without it. The pin beside a plugin in the Installed plugins list keeps it instead, so that JBrowse loads it every time you open it in this browser.

  • The list is per configuration, not per site. A plugin kept on jbrowse.org/code/jb2/main/?config=demos/hg002/config.json does not load on another demo, or on another version of the app.
  • It lives in this browser and nowhere else. A session you share carries none of it, and neither does the same JBrowse opened on another machine.
  • Tools → Permanent plugins... is the list itself, where one can be switched off without being removed, or taken out for good.
  • An admin editing config.json is installing for every visitor instead, so the pin does not appear in admin mode.

Because these load before anything is on screen, a plugin that crashes on load would otherwise take the app down on every visit with no way back to the menu. Two things stop that:

  • The fatal error dialog offers Reload without permanent plugins.
  • A load that never finishes turns them off by itself next time, and says which ones were loading. Tools → Permanent plugins... turns them back on once the culprit is switched off.

Adding ?safeMode to the URL does the same thing deliberately, and accuses nobody.

See also