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Plugins

TL;DR: in jbrowse-web and jbrowse-desktop, add a plugin by listing its name (which must match the name the plugin registers itself under) and bundle url in the top-level plugins array.

{
  "plugins": [
    {
      "name": "GDC",
      "url": "https://unpkg.com/jbrowse-plugin-gdc/dist/jbrowse-plugin-gdc.umd.production.min.js"
    },
    {
      "name": "MyPlugin",
      "esmLoc": { "uri": "plugin.js" }
    }
  ]
}
  • name must match the plugin's own registration (name = 'GDC' in the plugin class), or the plugin fails to load.
  • The plugin store lists unpkg URLs for published plugins, which you can also download to your own server. Plugin authors submit a PR to jbrowse-plugin-list.
  • Embedded components load plugins inline; see the inline plugins example.

url is the simplest field and equals umdUrl. The others differ in module format and in what the path resolves against:

FieldModule formatPath resolved relative to
urlUMDindex.html
umdUrlUMDindex.html
umdLocUMDconfig.json
esmUrlESMindex.html
esmLocESMconfig.json
cjsUrlCJSindex.html (desktop only)

umdLoc/esmLoc suit a plugin file that lives beside config.json, and cjsUrl is for jbrowse-desktop, since Electron does not load ESM.

Opening the plugin store from the Tools menu. Plugins installed via the config (here UMDUrlPlugin) show a lock icon in the Installed plugins section, indicating they cannot be removed through the GUI. The Available plugins list below offers one-click installs. 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.

See also