CyverseRemoteTracks is a plugin that loads JBrowse-compatible track configurations and data from resources hosted within the CyVerse Data Store.
This plugin is developed to work in conjunction with an app published within the CyVerse Discovery Environment,
called Deploy Community Tracks, that allows the Araport User Community members to upload
GFF3/BED/BAM/VCF formatted data files via the interface, which are pre-processed, indexed (using Tabix or SAMTools),
and stored in the CyVerse DE, along with supporting JBrowse track config files. The workflow also changes the ACLs on
these files to allow anonymous access.
The CyverseRemoteTracks plugin uses the Agave Files API to find all JBrowse tracks conf files located on the CyVerse Data Store and dynamically add these tracks to the Hierarchical Track List.
The CyverseRemoteTracks plugin can be enabled using either of the following methods (see official JBrowse documentation on using plugins):
tracks.conf
[plugins]
ComboTrackSelector.location += ./plugins/CyverseRemoteTracks
CyverseRemoteTracks.accessToken += <insert-agave-api-token-here>
CyverseRemoteTracks.filesApiBaseUrl += https://agave.iplantc.org/files/v2
CyverseRemoteTracks.storageSystemId += data.iplantcollaborative.org
CyverseRemoteTracks.anonFilesBaseUrl += https://de.cyverse.org/anon-files/iplant/home
CyverseRemoteTracks.configFilesPath += araport/community-tracks/shared
trackList.json
"plugins": [
{
"name += CyverseRemoteTracks",
"location": "./plugins/CyverseRemoteTracks",
"accessToken": "<insert-agave-api-token-here>",
"filesApiBaseUrl": "https://agave.iplantc.org/files/v2",
"storageSystemId": "data.iplantcollaborative.org",
"anonFilesBaseUrl": "https://de.cyverse.org/anon-files/iplant/home",
"configFilesPath": "araport/community-tracks/shared"
}
]
Once enabled and configured correctly, the CyverseRemoteTracks should appear as seen below:
- Vivek Krishnakumar - JCVI
If you have any questions regarding the usage of this plugin, please write to mailto:araport@jcvi.org