diff --git a/docs/assets/instances.png b/docs/assets/instances.png index bc5f89d..e3e62a7 100644 Binary files a/docs/assets/instances.png and b/docs/assets/instances.png differ diff --git a/docs/assets/manage_tracks.png b/docs/assets/manage_tracks.png index 846261b..00d7ef5 100644 Binary files a/docs/assets/manage_tracks.png and b/docs/assets/manage_tracks.png differ diff --git a/docs/assets/tracks_list.png b/docs/assets/tracks_list.png index 3d6bd4e..a87e674 100644 Binary files a/docs/assets/tracks_list.png and b/docs/assets/tracks_list.png differ diff --git a/docs/guide/jbrowse_mgmt/instances.rst b/docs/guide/jbrowse_mgmt/instances.rst index a1eb483..02e4912 100644 --- a/docs/guide/jbrowse_mgmt/instances.rst +++ b/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. diff --git a/docs/guide/jbrowse_mgmt/tracks.rst b/docs/guide/jbrowse_mgmt/tracks.rst index 0bc79b8..8f80958 100644 --- a/docs/guide/jbrowse_mgmt/tracks.rst +++ b/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.