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Gene JBrowse Fields

This module creates a field on Gene pages that features a JBrowse instance embedded in an iframe

The URL of the JBrowse instance in the iframe is configurable to fit most URL schemas. The JBrowse instance must already exist.

Instructions

Installation

  1. Install and enable this module in your normal place
  2. clear the cache: drush cc all

Configuration

  1. Navigate to admin/tripal/extension/gene_jbrowse_field/config in the browser to construct the URL. Use the tokens provided to ensure that the URL actually resolves to your JBrowse instance.

Enable Field

  1. Navigate to the Tripal 3 Content Type administration page for Gene type /admin/structure/bio_data/manage/ and click on "Manage Fields"
  2. Click "+ Check for new fields". It should find the local__jbrowse_link field
  3. On the "Manage Display" tab, drag the newly created JBrowse field to where you want it to display.

Progress/Task List

  • Get field, widget added
  • Get (any) data to show up in the field
  • Get desired info from database, construct iframe.
  • Remove hardcoded i5k-centric URL parameters
  • Generate secondary widget/formatter to let the admin choose how to display
    • JBrowse iframe
    • Link
  • Make links dynamically generated (possible to not have to read from DB each time?)
  • mRNA Page