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Integration

jbrowse-plugin-linkout

DOI

The plugin allows users to define where URLs combined with id to links to obtain genetic information according to their needs. For example, the plugin can automatically add link outs to the national center for biotechnology information (NCBI) feature page if a feature has NCBI ids on JBrowse 2 desktop or web.

Usage

DEMO Video

Please click the image below to watch the DEMO video.

vedio

Using in JBrowse 2 Desktop

1. Click TOOLS → Plugin store:

2. Click ADD CUSTOM PLUGIN:

3. Type Plugin name & Plugin URL → click SUBMIT:

You can copy it here:

  • Plugin name
Linkout
  • Plugin URL
https://unpkg.com/jbrowse-plugin-linkout/dist/jbrowse-plugin-linkout.umd.production.min.js

After that, you can see the Linkout in Installed plugins

4. Click on the icon with three dots on the right → click Setting:

5. Go to formatDetails in FeatureTrack settings in the block on the right:

6. Scroll right and you will see circles O:

7. After clicking the cycle, the circle will change to an X:

8. Type the setting of the feature or subfeatures based on your needs

The format is as follows:

  • feature
{dbxref:linkout({type_name_1: linkout_url_1, type_name_2: linkout_url_2}, feature)}
  • subfeatures
{dbxref:linkout({type_name_3: linkout_url_3, type_name_4: linkout_url_4}, feature)}

Like this:

Congratulations! You complete it!

For example:

The plugin that automatically adds link outs to the national center for biotechnology information (NCBI) feature page if a feature has NCBI ids on JBrowse.

  • feature
{dbxref:linkout({GeneID: 'https://www.ncbi.nlm.nih.gov/gene/'}, feature)}
  • subfeatures
{dbxref:linkout({GeneID: 'https://www.ncbi.nlm.nih.gov/gene/', Genbank: 'https://www.ncbi.nlm.nih.gov/nuccore/'}, feature)}

You can click the GeneID:126871197 or Genbank:XR_007691556.1 in dexref on the right:

Using in JBrowse 2 Web

1. Add to the plugins of your JBrowse Web config:

{
  "plugins": [
    {
      "name": "Linkout",
      "url": "https://unpkg.com/jbrowse-plugin-linkout/dist/jbrowse-plugin-linkout.umd.production.min.js"
    }
  ]
}

2. Add to the formatDetails in tracks of your JBrowse Web config:

"tracks": [
    {
      "formatDetails": {
        "feature": "jexl: {dbxref:linkout({type_name_1: linkout_url_1}, feature)}",
        "subfeatures": "jexl: {dbxref:linkout({type_name_2: linkout_url_2}, feature)}"
      }
    }
  ]