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isb-cgc · Dec 28, 2015 · 230c110 · 230c110
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diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/sections/Web-UI.doctree b/docs/build/doctrees/sections/Web-UI.doctree
diff --git a/docs/build/html/_sources/sections/Web-UI.txt b/docs/build/html/_sources/sections/Web-UI.txt
@@ -6,13 +6,14 @@ Documentation for the ISB-CGC web app is available from within the web-app.  Aft
 click on the down-arrow next to your name in the upper-right corner and select "Help".
 
 .. toctree::
+   :maxdepth: 1
 
-  webapp/releases
-  webapp/User-Dashboard
-  webapp/Cohorts
-  webapp/Visualizations
-  webapp/SeqPeek
-  webapp/IGV-Browser
-  webapp/Sharing
-  webapp/General-Permissions
+   webapp/releases
+   webapp/User-Dashboard
+   webapp/Cohorts
+   webapp/Visualizations
+   webapp/SeqPeek
+   webapp/IGV-Browser
+   webapp/Sharing
+   webapp/General-Permissions
 
diff --git a/docs/build/html/sections/Web-UI.html b/docs/build/html/sections/Web-UI.html
@@ -58,90 +58,12 @@ <h1>Web Interface<a class="headerlink" href="#web-interface" title="Permalink to
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="webapp/releases.html">Release Notes</a></li>
-<li class="toctree-l1"><a class="reference internal" href="webapp/User-Dashboard.html">User Dashboard</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="webapp/User-Dashboard.html#create-cohorts-and-visualizations">Create Cohorts and Visualizations</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#create-a-cohort">Create a cohort</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#create-a-general-visualization">Create a general visualization</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#create-a-seqpeek-visualization">Create a SeqPeek visualization</a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/User-Dashboard.html#operations-on-cohorts-and-visualizations">Operations on Cohorts and Visualizations</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#delete-a-cohort-or-a-visualization">Delete a Cohort or a Visualization</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#share-a-cohort-or-a-visualization">Share a Cohort or a Visualization</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#set-operations-on-cohorts">Set Operations on Cohorts</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#your-cohorts">Your Cohorts</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#your-visualizations">Your Visualizations</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#your-seqpeeks">Your SeqPeeks</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#searching">Searching</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/User-Dashboard.html#sorting">Sorting</a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="webapp/Cohorts.html">Cohorts</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Cohorts.html#creating-and-saving-a-cohort">Creating and saving a cohort</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="webapp/Cohorts.html#cohort-creation-page">Cohort Creation Page</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="webapp/Cohorts.html#cohort-filters">Cohort Filters</a><ul>
-<li class="toctree-l5"><a class="reference internal" href="webapp/Cohorts.html#participant-filters-list">Participant Filters List</a></li>
-<li class="toctree-l5"><a class="reference internal" href="webapp/Cohorts.html#data-type-filters-list">Data Type Filters List</a></li>
-<li class="toctree-l5"><a class="reference internal" href="webapp/Cohorts.html#selected-filters-panel">Selected Filters Panel</a></li>
-<li class="toctree-l5"><a class="reference internal" href="webapp/Cohorts.html#clinical-features-panel">Clinical Features Panel</a></li>
-<li class="toctree-l5"><a class="reference internal" href="webapp/Cohorts.html#data-availability-panel">Data Availability Panel</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Cohorts.html#operations-on-cohorts">Operations on Cohorts</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="webapp/Cohorts.html#set-operations">Set Operations</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/Cohorts.html#editing-a-cohort">Editing a Cohort</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="webapp/Cohorts.html#main-menu">Main Menu</a></li>
-<li class="toctree-l4"><a class="reference internal" href="webapp/Cohorts.html#id1">Selected Filters Panel</a></li>
-<li class="toctree-l4"><a class="reference internal" href="webapp/Cohorts.html#details-panel">Details Panel</a></li>
-<li class="toctree-l4"><a class="reference internal" href="webapp/Cohorts.html#id2">Clinical Features Panel</a></li>
-<li class="toctree-l4"><a class="reference internal" href="webapp/Cohorts.html#id3">Data Availability Panel</a></li>
-<li class="toctree-l4"><a class="reference internal" href="webapp/Cohorts.html#commenting">Commenting</a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/Cohorts.html#deleting-a-cohort">Deleting a cohort</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/Cohorts.html#creating-a-cohort-from-a-visualization">Creating a Cohort from a Visualization</a></li>
-<li class="toctree-l3"><a class="reference internal" href="webapp/Cohorts.html#copying-a-cohort">Copying a cohort</a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="webapp/Visualizations.html">Visualizations</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Visualizations.html#create">Create</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Visualizations.html#save">Save</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Visualizations.html#delete">Delete</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Visualizations.html#copy">Copy</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Visualizations.html#add-plot">Add Plot</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Visualizations.html#delete-plot">Delete Plot</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Visualizations.html#plot-comments">Plot Comments</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Visualizations.html#edit-plot">Edit Plot</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="webapp/Visualizations.html#selecting-new-feature-s">Selecting new Feature(s)</a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Visualizations.html#pairwise-statistical-test">Pairwise Statistical Test</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="webapp/SeqPeek.html">SeqPeek</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="webapp/SeqPeek.html#creating-a-seqpeek-visualization">Creating a SeqPeek Visualization</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/SeqPeek.html#saving-a-seqpeek-visualization">Saving a SeqPeek Visualization</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/SeqPeek.html#deleting-a-seqpeek-visualization">Deleting a SeqPeek Visualization</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="webapp/IGV-Browser.html">Integrative Genomics Viewer</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="webapp/IGV-Browser.html#accessing-the-igv-browser">Accessing the IGV Browser</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="webapp/Sharing.html">Sharing Cohorts and Visualizations</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Sharing.html#sharing-a-cohort">Sharing a cohort</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Sharing.html#sharing-a-visualization">Sharing a visualization</a></li>
-<li class="toctree-l2"><a class="reference internal" href="webapp/Sharing.html#sharing-a-seqpeek-visualization">Sharing a SeqPeek visualization</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="webapp/User-Dashboard.html">User Dashboard</a></li>
+<li class="toctree-l1"><a class="reference internal" href="webapp/Cohorts.html">Cohorts</a></li>
+<li class="toctree-l1"><a class="reference internal" href="webapp/Visualizations.html">Visualizations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="webapp/SeqPeek.html">SeqPeek</a></li>
+<li class="toctree-l1"><a class="reference internal" href="webapp/IGV-Browser.html">Integrative Genomics Viewer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="webapp/Sharing.html">Sharing Cohorts and Visualizations</a></li>
 <li class="toctree-l1"><a class="reference internal" href="webapp/General-Permissions.html">General Permissions</a></li>
 </ul>
 </div>

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -109,8 +109,8 @@
 .. container:: isbcgcfooter
 
   Have feedback or corrections?  All improvements to these docs are welcome!
-  You can file an issue `here <https://github.com/isb-cgc/readthedocs/issues>`_
-  or email us at feedback@isb-cgc.org.
+
+  You can file an issue `here <https://github.com/isb-cgc/readthedocs/issues>`_ or email us at feedback@isb-cgc.org.
 
 .. GLOBAL LINK REPLACEMENTS CAN GO HERE
 

diff --git a/docs/source/sections/Web-UI.rst b/docs/source/sections/Web-UI.rst
@@ -6,13 +6,14 @@ Documentation for the ISB-CGC web app is available from within the web-app.  Aft
 click on the down-arrow next to your name in the upper-right corner and select "Help".
 
 .. toctree::
+   :maxdepth: 1
 
-  webapp/releases
-  webapp/User-Dashboard
-  webapp/Cohorts
-  webapp/Visualizations
-  webapp/SeqPeek
-  webapp/IGV-Browser
-  webapp/Sharing
-  webapp/General-Permissions
+   webapp/releases
+   webapp/User-Dashboard
+   webapp/Cohorts
+   webapp/Visualizations
+   webapp/SeqPeek
+   webapp/IGV-Browser
+   webapp/Sharing
+   webapp/General-Permissions