Merge pull request #24 from tripal/update-docs

Updated documentation

docs/Makefile

@@ -4,6 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = TripalJBrowse
 SOURCEDIR     = .
 BUILDDIR      = _build
 
@@ -16,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/install.rst → docs/guide/install.rst

@@ -1,4 +1,3 @@
-
 Installation
 =============
 
@@ -6,4 +5,6 @@ Installation
    :maxdepth: 2
    :caption: Contents:
 
-   install/tripal_jbrowse
+   install/dependencies
+   install/jbrowse_mgmt
+   install/instance_page

docs/guide/install/dependencies.rst

@@ -0,0 +1,7 @@
+Dependencies
+============
+
+Please ensure that the following are installed on your server:
+
+- `JBrowse <http://gmod.org/wiki/JBrowse_Configuration_Guide>`_.
+- `Tripal <http://tripal.info>`_

docs/tripal_jbrowse/instance_page.rst → docs/guide/install/instance_page.rst

@@ -1,6 +1,5 @@
-
-JBrowse Instance Page
-======================
+JBrowse Page Integration
+========================
 
 This guide will show you **how to create a page within your Tripal site for an existing JBrowse instance**. This ensures a *consistent user experience* by making the menu system of the Tripal site available to the user while browsing. If the user needs more space they can choose the *FullScreen option* to remove the menus.
 
@@ -14,19 +13,19 @@ This guide will show you **how to create a page within your Tripal site for an e
 
 You create a JBrowse Instance page by navigating to **Content > Add Content > JBrowse Instance** on the Administration Toolbar. Then just fill out the form and click save!
 
-.. image:: instancepage.1.addcontent.png
+.. image:: ../../assets/instancepage.1.addcontent.png
 
-.. image:: instancepage.2.addinstance.png
+.. image:: ../../assets/instancepage.2.addinstance.png
 
 The **title** will become the title of the page and the **description** will be shown above the JBrowse instances. The description is a good place to add any warnings or instructions.
 
-.. image:: instancepage.3.createtop.png
+.. image:: ../../assets/instancepage.3.createtop.png
 
 The **Existing JBrowse URL** is the URL to the JBrowse instance you want to embed. You should be able to put this URL into your browser and access the JBrowse instance directly, even in the case of local instances.
 
 The **Start Locations** allows you to specify where you want the JBrowse to navigate to for first time users. Keep in mind that JBrowse caches user location and thus all subsequent times a user accesses the instance it will start at their last browsed location.
 
-.. image:: instancepage.4.createbottom.png
+.. image:: ../../assets/instancepage.4.createbottom.png
 
 The **Tracks** allows you to set which tracks you want shown by default. You should enter the machine name of the tracks here with multiple tracks separated by comma's.
 

docs/guide/install/jbrowse_mgmt.rst

@@ -0,0 +1,9 @@
+Tripal JBrowse Management
+=========================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   jbrowse_mgmt/install
+   jbrowse_mgmt/configuration

docs/guide/install/jbrowse_mgmt/configuration.rst

@@ -0,0 +1,8 @@
+Tripal JBrowse 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.
+
+.. image:: ../../../assets/settings_page.png

docs/install/tripal_jbrowse.rst → docs/guide/install/jbrowse_mgmt/install.rst

@@ -1,15 +1,14 @@
-
 Tripal JBrowse Installation
 ============================
 
 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.
+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.
+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:: tripal_jbrowse.1.install.png
+.. image:: ../../../assets/tripal_jbrowse.1.install.png
 
 .. note::
 
-   This module is dependant upon the **Link** module. It is not mentioned above in the install instructions since you should already have installed it when installing Tripal.
+   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.

docs/guide/jbrowse_mgmt.rst

@@ -0,0 +1,9 @@
+Tripal JBrowse Management
+=========================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   jbrowse_mgmt/instances
+   jbrowse_mgmt/tracks

docs/guide/jbrowse_mgmt/instances.rst

@@ -0,0 +1,21 @@
+Managing Instances
+==================
+
+Listing and Creating Instances
+------------------------------
+
+To list all instances, visit ``/admin/tripal_jbrowse``.
+
+.. image:: ../../assets/instances.png
+
+
+Creating Instances
+------------------
+
+As highlighted on the screenshot above, you can create new instances by clicking the "Add New Instance" 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.

docs/guide/jbrowse_mgmt/tracks.rst

@@ -0,0 +1,25 @@
+Managing Tracks
+===============
+
+Creating and Deleting Tracks
+----------------------------
+
+To create a new track, you need visit the instances list page and click Manage Tracks.
+
+.. image:: ../../assets/manage_tracks.png
+
+The manage tracks link, will lead to a page where you can create and delete tracks (see screenshot below).
+
+.. image:: ../../assets/tracks_list.png
+
+.. warning::
+    Please note that files don't get automatically removed. You have to manually remove the track files yourself.
+
+
+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.
+
+To edit a track, simply click the manage track button on the "manage tracks" page as shown on the screenshot above.

docs/index.rst

@@ -1,6 +1,11 @@
+.. Tripal JBrowse documentation master file, created by
+    sphinx-quickstart on Mon Nov 19 08:36:56 2018.
+    You can adapt this file completely to your liking, but it should at least
+    contain the root `toctree` directive.
 
-Tripal JBrowse Documentation
-=============================
+
+Tripal JBrowse
+==============
 
 This package of modules integrates `GMOD JBrowse <https://jbrowse.org/>`_ into your `Tripal <http://tripal.info/>`_ site providing
 
@@ -10,8 +15,7 @@ This package of modules integrates `GMOD JBrowse <https://jbrowse.org/>`_ into y
  This powerful combination allows you to provide seamless genome browsing to your users in an administrator-friendly manner.
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+    :maxdepth: 2
 
-   install
-   tripal_jbrowse
+    guide/install
+    guide/jbrowse_mgmt

docs/tripal_jbrowse.rst

@@ -1,13 +0,0 @@
-
-Tripal JBrowse Page Integration
-================================
-
-.. note::
-
-   The following functionality is provided by the **Tripal JBrowse Integration** sub-module.
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Functionality:
-
-   tripal_jbrowse/instance_page