Browse Source

Update jbrowse management for registering instances.

Lacey Sanderson 5 years ago
parent
commit
7623da2db1

BIN
docs/assets/instances.png


BIN
docs/assets/manage_tracks.png


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docs/assets/tracks_list.png


+ 22 - 3
docs/guide/jbrowse_mgmt/instances.rst

@@ -4,7 +4,7 @@ Managing Instances
 Listing and Creating 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
 .. image:: ../../assets/instances.png
 
 
@@ -12,10 +12,29 @@ To list all instances, visit ``/admin/tripal_jbrowse``.
 Creating Instances
 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
 Deleting Instances
 ------------------
 ------------------
 
 
 To delete an instance, you must first visit the instances list page and clicking the delete instance link.
 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.

+ 2 - 3
docs/guide/jbrowse_mgmt/tracks.rst

@@ -4,7 +4,7 @@ Managing Tracks
 Creating and Deleting 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
 .. 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
 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.
 To edit a track, simply click the manage track button on the "manage tracks" page as shown on the screenshot above.