arabidopsis-information-portal / combotrackselector Goto Github PK

ComboTrackSelector is a JBrowse plugin that enables both the Hierarchical and Faceted track selectors to co-exist within the scope of JBrowse. The plugin allows for the segregation of the available tracks between the two selectors, which can be customized based on amount of track metadata (e.g. tracks with multiple metadata aspects/facets can be restricted to the Faceted selector only).

The following steps explain how the ComboTrackSelect plugin can be installed and configured to work with JBrowse:

• First, prepare a trackList.json file for tracks which should appear only in the Hierarchical track selector. An example of such a config file used by the Araport project: trackList.json

• Second, prepare a trackList2.json file for tracks which should appear only in the Faceted track selector. An example of such a config file as used by the Araport project: trackList2.json

• Third, prepare a csv or json formatted file of track metadata, associated with the set of tracks set up to appear in the Faceted selector. Examples of such config files as used by the Araport project: epiccogeMetaData.csv or epiccogeMetaData.json.
  The trackList2.json config file should have an appropriately configured trackMetadata: { } stanza like so:

    {
    	"tracks" : {},
    	"dataRoot" : "arabidopsis",
    	"trackMetadata": {
    		"sources": [
    		{
    			"url": "{dataRoot}/epiccogeMetaData.json",
    			"type": "json"
    		}
    	],
    	"indexFacets": [
    		"Lab Name",
    		"Type",
    		"Platform",
    		:
    		:
    	]
    	}
    }
  

• Finally, the plugin can be enabled using either ONE OF the following methods (see official JBrowse documentation on using plugins):

tracks.conf

	[plugins]
	ComboTrackSelector.location += ./plugins/ComboTrackSelector
	ComboTrackSelector.icon += https://gravatar.com/avatar/f5ae7bbffab5fbd56777fee2720c7ee4.png

trackList.json

	"plugins": [
		{
			"name" : "ComboTrackSelector",
			"location" : "./plugins/ComboTrackSelector",
			"icon" : "https://gravatar.com/avatar/f5ae7bbffab5fbd56777fee2720c7ee4.png"
		}
	]

Once enabled and configured correctly, the ComboTrackSelector should appear as seen below:

• Maria Kim - JCVI
• Vivek Krishnakumar - JCVI

If you have any questions regarding the usage of this plugin, please write to mailto:[email protected]