Update jbrowse management for registering instances.

docs/guide/jbrowse_mgmt/instances.rst

@@ -4,7 +4,7 @@ Managing Instances
 Listing and Creating Instances
 ------------------------------
 
-To list all instances, visit ``/admin/tripal_jbrowse``.
+To list all instances, visit Administration » Tripal » Extensions » Tripal JBrowse Management.
 
 .. image:: ../../assets/instances.png
 
@@ -12,10 +12,29 @@ To list all instances, visit ``/admin/tripal_jbrowse``.
 Creating Instances
 ------------------
 
-As highlighted on the screenshot above, you can create new instances by clicking the "Add New Instance" link.
+As highlighted on the screenshot above, you can create new instances by clicking the "Create New Instance" link. This will create a new data directory based on the organism choosen. All instances created will use the same JBrowse installation, which makes it easier to update JBrowse.
+
+Registering Existing Instances
+--------------------------------
+
+You can also register existing JBrowse instances with this module. To do so
+1. Create a symbolic link in your configured data directory where the name of the link matches the organism it is for: ``genus_species__common_name``.
+2. Click on "Register Existing Instance" as highlighted on the screenshot above.
+3. Fill out the form to describe the existing JBrowse instance.
+
+.. note::
+
+  If you would like to move an existing instance to the JBrowse managed by this module permanently then copy the data directory rather then creating a symbolic link.
 
 Deleting Instances
 ------------------
 
 To delete an instance, you must first visit the instances list page and clicking the delete instance link.
-Note that the actual files for the instance are not deleted. You will need to delete all files manually.
+
+.. warning::
+
+  The actual files for the instance are not deleted. You will need to delete all files manually.
+
+.. note::
+
+  If you accidentally delete an instance, you can use the "Register Existing Instance" process to re-register it with the system. All previously created tracks will no longer be able to be managed but you will be able to add new tracks, etc.

docs/guide/jbrowse_mgmt/tracks.rst

@@ -4,7 +4,7 @@ Managing Tracks
 Creating and Deleting Tracks
 ----------------------------
 
-To create a new track, you need visit the instances list page and click Manage Tracks.
+To create a new track, you need visit the instances list page (Administration » Tripal » Extensions » Tripal JBrowse Management) and click Manage Tracks.
 
 .. image:: ../../assets/manage_tracks.png
 
@@ -19,7 +19,6 @@ The manage tracks link, will lead to a page where you can create and delete trac
 Editing Tracks
 --------------
 
-This modules allows you to configure a track after it has been created. This provides a way to
-add the track to a category, change the colors and type of the track amongst other configuration options.
+This modules allows you to configure a track after it has been created. This provides a way to add the track to a category, change the colors and type of the track amongst other configuration options.
 
 To edit a track, simply click the manage track button on the "manage tracks" page as shown on the screenshot above.