Merge pull request #39 from tripal/31-improve_docs

Update the documentation to match the current state of the module

docs/guide/install/instance_page.rst

@@ -3,12 +3,5 @@
 
 This module is available for download from github.com/tripal/tripal_jbrowse.
 
-1. Download and upack the module into ``[DRUPAL ROOT]/sites/all/modules`` where ``DRUPAL_ROOT`` is the path to your Drupal site.
-2. Navigate to ``https://yourdrupalsite.com/admin/modules`` or click **Administration Toolbar > Modules**
-3. Scroll to **Tripal Extensions**, click the checkbox beside "Tripal JBrowse Integration", and click the "Save Configuration" button at the bottom of the page.
-
-.. image:: ../../assets/tripal_jbrowse.1.install.png
-
-.. note::
-
-   This module is dependent upon the **Link** module. It is not mentioned above in the install instructions since you should already have installed it when installing Tripal.
+1. First install :doc:`Tripal JBrowse Management <jbrowse_mgmt>`
+2. Run ``drush en -y tripal_jbrowse_page`` or enable through the modules page

docs/guide/install/jbrowse_mgmt/configuration.rst

@@ -2,7 +2,8 @@ Configuration
 ===============
 
 In order for the module to function properly, you need to first configure it.
-Please visit ``http://YOUR_SITE/admin/tripal_jbrowse/configure`` (replace YOUR_SITE with your domain)
-and fill out the form. You will need to know information about your JBrowse information.
+
+1. Visit your site through the browser and navigate to Administration » Tripal » Extensions » Tripal JBrowse Management » Settings.
+2. Fill out the configuration form and click "Save Settings". **You will need to know information about your JBrowse instance.**
 
 .. image:: ../../../assets/settings_page.png

docs/guide/install/jbrowse_mgmt/install.rst

@@ -2,8 +2,8 @@ Installation
 ==============
 
 1. Download the module to your Drupal modules folder
-2. Run drush en -y hardwoods_jbrowse or enable through the modules page
-3. Visit the configuration page at /admin/hardwoods_jbrowse/configure
+2. Run ``drush en -y tripal_jbrowse_mgmt`` or enable through the modules page
+3. Visit the configuration page at Administration » Tripal » Extensions » Tripal JBrowse Management » Settings
 
 .. note::
 

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.

docs/index.rst

@@ -9,8 +9,8 @@ Tripal JBrowse
 
 This package of modules integrates `GMOD JBrowse <https://jbrowse.org/>`_ into your `Tripal <http://tripal.info/>`_ site providing
 
-   - Tripal page integration via **Tripal JBrowse** and
-   - a user interface for JBrowse instance creation and management via **Tripal JBrowse Management**.
+  1. A user interface for JBrowse instance creation and management via **Tripal JBrowse Management**
+  2. Drupal menu links and pages with embedded JBrowse instances via  **Tripal-JBrowse Page Integration**
 
  This powerful combination allows you to provide seamless genome browsing to your users in an administrator-friendly manner.