Edited all admin help pages

tripal_analysis/theme/tripal_analysis_admin.tpl.php

@@ -1,115 +1,45 @@
 
-  <h3>Tripal Analysis Administrative Tools Quick Links:</h3>
+<h3>Tripal Analysis Administrative Tools Quick Links:</h3>
+<ul>
+ <li><?php print l('Analysis Configuration', "admin/tripal/tripal_analysis/configuration") ?></li>
+</ul>
+
+
+<h3>Module Description:</h3>
+<p>The Tripal Analysis module provides a new analysis content type that is intended to be
+  used when a more specialized analysis module does not exist.  Because it is generic, it does not
+  provide any visualization or data loading tools for analysis data.  Specialized analysis modules,
+  such as the Tripal Analysis Blast or Tripal Analysis KEGG modules provide loading and custom
+  visualizations for the analysis results.  These modules must be installed separately.
+</p>
+
+<h3>Setup Instructions:</h3>
+<p>After installation of the analysis module or any specialized analysis module.  The following tasks should be performed
+<ol>
+  <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
+   or administer analyses. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
+   permissions under the 'tripal_analysis' section as appropriate for your site. For a simple setup, allow anonymous 
+   users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
+
+
+<li><p><b>Create an Analysis</b>:  An analysis should be <?php print l('created', 'node/add/chado-analysis')?> before 
+data is imported into chado.  The generic analysis type should only be used when a more specialized analysis module
+(e.g. Tripal Analysis Blast module) does not already exists.  All data imported into Chado should be associated with 
+an analysis to help keep track of the source for data.</p></li>
+
+<li><p><b>Sync Analyses</b>:  If you have analyses already stored in Chado and would like to create pages for them, then
+analyses can be synced using the
+ <?php print l('analysis configuration page', 'admin/tripal/tripal_analysis/configuration') ?>. The process of 'syncing'
+ automatically creates the pages as if you had created them using the step above.
+</p></li>
+</ol>
+</p>
+
+<h3>Additional Features of this Module:</h3>
   <ul>
-             <li><a href="<?php print url("admin/tripal/tripal_analysis/configuration") ?>">Analysis Configuration</a></li>
-           </ul>
-
-
-  <h3>Module Description:</h3>
-  <p>The Tripal Analysis module provides a generic analysis content type that is intended to be
-            used when a more specialized analysis module does not exist.  Because it is generic, it does not
-            provide any visualization or data loading tools for analysis data.  Specialized analysis modules,
-            such as the Tripal Analysis Blast or Tripal Analysis KEGG modules provide loading and custom
-            visualizations for the analysis results.  These modules must be installed separately.
-            </p>
-
-  <h3>Setup Instructions:</h3>
-  <p>After installation of the analysis module or any specialized analysis module.  The following tasks should be performed
-            <ol>
-              <li><p><b>Set Permissions</b>: Each analysis module supports the Drupal user permissions interface for
-               controlling access to the content and functions. These permissions include viewing,
-               creating, editing or administering of
-               analysis content. The default is that only the original site administrator has these
-               permissions.  You can <a href="<?php print url('admin/user/roles') ?>">add roles</a> for classifying users,
-               <a href="<?php print url('admin/user/user') ?>">assign users to roles</a> and
-               <a href="<?php print url('admin/user/permissions') ?>">assign permissions</a> for the analysis content to
-               those roles.  For a simple setup, allow anonymous users access to view organism content and
-               allow the site administrator all other permissions.</p></li>
-
-
-               <li><p><b>Create Analysis</b>:  An analysis should be <a href="<?php print url('node/add') ?>">created</a> before data is imported into
-               chado.  The generic analysis type should only be used when a more specialized analysis module
-               (e.g. Tripal Analysis Blast module) does not already exists.  All data imported into
-               Chado should be associated with an analysis.
-
-               <li><p><b>Sync Analyses</b>:  If Chado has preloaded analyses then you can sync those.  This process is what
-               creates the pages for viewing an analysis on the site.  Analyses can be synced using the
-               <a href="<?php print url('admin/tripal/tripal_analysis/configuration') ?>">Analysis Configuration page</a>.
-               However, syncing an analyses will always create a generic analysis content type.  If you would like
-               to use a specialized analysis module for visualization of data then do not sync the analysis but recreate it
-               using the appropriate specialized analysis content type.</p></li>
-
-            </ol>
-            </p>
-
-
-  <h3>Features of this Module:</h3>
-  <p>Aside from providing a generic content type the Tripal Analysis module also provides the following functionality
-            <ul>
-
-              <li><p><b>Basic Analysis Lookup View</b>: This module provides a basic <a href="<?php print url('analyses') ?>">analysis search
-              tool</a> for finding or listing analyses in Chado. It does not require indexing for Drupal searching but relies
-              on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a> must be installed. </p></li>
-
-            </ul>
-            </p>
-
-  <h3>Page Customizations</h3>
-  <p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
-             Below is a description of several methods.  These methods may be used in conjunction with one another to
-             provide fine-grained control.
-             <ul>
-
-             <li><p><b>Integration with Drupal Panels</b>:  <a href="http://drupal.org/project/views">Drupal Panels</a>
-              allows for customization of a page layout if you don\'t want to do PHP/Javascript/CSS programming.
-              Tripal comes with pre-set layouts for analysis pages.  However,
-              Panels become useful if you prefer a layout that is different from the pre-set layouts.  Chado content
-              is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the
-              Panel\'s GUI.</p></li>
-
-             <li><p><b>Drupal\'s Content Construction Kit (CCK)</b>: the
-             <a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a> is a powerful way to add non-Chado content
-             to any page without need to edit template files or knowing PHP.  You must first download and install CCK.
-             With CCK, the site administartor can create a new field to appear on the page.  For example, currently,
-             the Chado publication module is not yet supported by Tripal.  Therefore, the site administrator can add a text
-             field to the analysis pages.  This content is not stored in Chado, but will appear on the analysis page.  A field
-             added by CCK will also appear in the form when editing a analysis to allow users to manually enter the appropriate
-             text.  If the default pre-set layout and themeing for Tripal is used, it is better to create the CCK element,
-             indicate that it is not to be shown (using the CCK interface), then manually add the new content type
-             where desired by editing the templates (as described below).  If using Panels, the CCK field can be added to the
-             location desired using the Panels interface.</p></li>
-
-             <li><p><b>Drupal Node Templates</b>:  The Tripal packages comes with a "theme_tripal" directory that contains the
-             themeing for Chado content.    The analysis module has a template file for analysis "nodes" (Tripal analysis pages).  This file
-             is named "node-chado_analysis.tpl.php", and provides javascript, HTML and PHP code for display of the analysis
-             pages.  Specialized analysis modules will have their own template files as well, such as "node-chado_analysis-blast.tpl.php" for the
-             Tripal Analysis Blast module.  You can edit the template file to control which types of information (or which analysis "blocks") are displayed
-             for analysis. Be sure to
-             copy these template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
-             future Tripal updates may overwrite your customizations. See the <a href="http://tripal.sourceforge.net/">Tripal website </a>
-             for instructions on how to access variables and other Chado content within the template file.</p></li>
-
-             <li><p><b>Analysis "Block" Templates</b>:  In the "theme_tripal" directory are subdirectories named after each tripal module (e.g. "tripal_feature", "tripal_library", etc.).
-             Inside each directory is a set of templates that control distinct types of information for each content type.  For example,
-             there is a "base" template for displaying of data directly from the Chado feature table, and a "references"
-             template for showing external site references for a feature (data from the feature_dbxref table).
-              These templates are used both by Drupal blocks
-             for use in Drupal Panels (as described above) or for use in the default pre-set layout that the node template
-             provides (also desribed above).  Analyses block templates can exist in any of these directories.  For example, the Tripal Analysis Unigene
-             module uses templates in the tripal_analysis_unigene, tripal_organism, and tripal_feature directories.  Content for a unigene is then
-             cusotmizable within each of these contexts.
-             You can customize block template as you desire.  Be sure to copy the
-             template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
-             future Tripal updates may overwrite your customizations.  See the <a href="http://tripal.sourceforge.net/">Tripal website </a>
-             for instructions on how to access variables and other Chado content within the template files.</p></li>
-             </li>
-
-             <li><p><b>Adding Links to the "Resources" Sidebar</b>: If you use the pre-set default Tripal layout for theming, you
-             will see a "Resources" sidebar on each page.  The links that appear on the sidebar are automatically generated
-             using Javascript for all of the analysis "Blocks" that appear on the page. If you want to add additional links
-             (e.g. a dynamic link to GBrowse for the analysis) and you want that link to appear in the
-             "Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the
-             section at the bottom of the template file where the resources section is found.</p></li>
-
-             </ul>
-             </p>
+    <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/analyses') ?> is provided for 
+    finding analyses. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
+    which must be installed to see the search tool.  Look for it in the navigation menu under the item 
+    "Search Biological Data". </p></li>
+</ul>
+</p>

tripal_core/theme/tripal_core_customize.tpl.php

@@ -0,0 +1,67 @@
+<p>Tripal was designed to allow for maiximum customization of content and the look-and-feel of the site.  By default,
+Tripal provides a suite of Drupal style templates that provide a generic presentation of data from a Chado database. 
+There are many options for customizing the look and feel of Tripal. Some customizations can be done without any
+programming whatsoever.  However, for advanced customizations, Tripal provides a robust API to allow a programmer
+to easily interact (select, update, delete, insert) data from a Chado database in whatever custom way desired.</p>
+
+<li><p><b>Integration with Drupal Views</b>: <a href="http://drupal.org/project/views">Drupal Views</a> is
+a powerful tool that allows the site administrator to create lists or basic searching forms of Chado content.
+It provides a graphical interface within Drupal to allow the site admin to directly query the Chado database
+and create custom lists without PHP programming or customization of Tripal source code.  Views can also
+be created to filter content that has not yet been synced with Druapl in order to protect access to non
+published data (only works if Chado was installed using Tripal).  If you have Views installed and enabled
+You can see a list of available pre-existing
+Views <a href="' . url('admin/build/views/') ?>">here</a>, as well as create your own. All Chado tables have 
+been exposed to Drupal Views</p></li>
+
+<h3>Customizations Without Programming</h3>
+<p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
+Below is a description of several methods.  These methods may be used in conjunction with one another to
+provide fine-grained control.
+<ul>
+
+<li><p><b>Integration with Drupal Panels</b>:  <a href="http://drupal.org/project/views">Drupal Panels</a>
+allows for customization of a page layout. Tripal comes with pre-set layouts for project pages.  However,
+Panels become useful if you prefer a layout that is different from the pre-set layouts.  Chado content
+is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the
+Panel\'s GUI.</p></li>
+
+<li><p><b>Drupal\'s Content Construction Kit (CCK)</b>: the
+<a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a> is a powerful way to add non-Chado content
+to any page without need to edit template files or knowing PHP.  You must first download and install CCK.
+With CCK, the site administartor can create a new fields to appear on any Tripal node page.  
+A field added by CCK will appear in the form when editing to allow users to manually enter the appropriate
+text.  These field values are not stored in Chado, but will appear on the page when saved. 
+If you are using the default themeing provided by Tripal, then it is better to create the CCK element,
+indicate that it is not to be shown (using the CCK interface), then manually add the new fields
+where desired by editing the templates (see section below about customizing through programming).  
+If using Panels, the CCK field can be added to the location desired using the Panels interface.</p></li>
+
+<li><p><b>Adding Links to the "Resources" Sidebar</b>: You can add new items to the resources side-bar of any Tripal node using the 
+<a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a>module and adding new field types to Tripal node types.  Instructions for adding these fields can be found
+on the <?php l('Tripal v1.0 Tutorial', 'http://www.gmod.org/wiki/Tripal_Tutorial_(v1.0)#Adding_Additional_Resources')?>  </p></li>
+</li>
+
+</ul>
+
+<h3>Customizations Through Programming</h3>
+<ul>
+<li><p><b>Adding Links to the "Resources" Sidebar</b>: If you use the pre-set default Tripal layout for theming, you
+will see a "Resources" sidebar on each page.  The links that appear on the sidebar are automatically generated
+using Javascript for all of the project "Blocks" that appear on the page. If you want to add additional links
+(e.g. a link to a views table showing all features of the current project) and you want that link to appear in the
+"Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the
+section at the bottom of the template file where the resources section is found.</p></li>
+
+<li><p><b>Editing Templates and Creating Custom Extension Modules</b>:There are several ways to customize the look-and-feel
+  for the way Chado data is presented through Tripal.
+  See the <a href="http://www.gmod.org/wiki/Tripal_Developer's_Handbook">Developers Handbook</a> for further infromation.   
+</p>
+
+<li><p><b>Sharing your customizations</b>: If you create a custom extension module that uses the Tripal API in
+accordance with the instructions in the Developers Handbook you can share your modules with other Tripal users.
+To share you module, you must first create a project account with Drupal and upload your extension module there. 
+Next, subscribe to the <a href="https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel">Tripal Developer's Mailing List
+</a> and send an email to the group indicating you have a new extension module and would like to share it.  A list of 
+extension modules that properly follow the Tripal API will be listed on the Tripal website for others to easily find.</p></li>
+</ul>

tripal_core/tripal_core.module

@@ -98,6 +98,13 @@ function tripal_core_menu() {
     'file' => 'system.admin.inc',
     'file path' => drupal_get_path('module', 'system'),
   );
+  $items['admin/tripal/customize'] = array(
+    'title' => 'Customize Tripal',
+    'position' => 'right',
+    'page callback' => 'theme',
+    'page arguments' => array('tripal_core_customize'),
+    'access arguments' => array('administer site configuration'),
+  );
   $items['tripal_toggle_box_menu/%/%/%'] = array(
     'title' => 'Toggle Box',
     'page callback' => 'tripal_toggle_box_menu',
@@ -250,8 +257,13 @@ function tripal_core_perm() {
 function tripal_core_theme() {
   return array(
     'tripal_core_job_view' => array(
-       'arguments' => array('job_id' => NULL),
-       'template' => 'tripal_core_job_view',
+      'arguments' => array('job_id' => NULL),
+      'template' => 'tripal_core_job_view',
+    ),
+    'tripal_core_customize' => array(
+      'arguments' => array('job_id' => NULL),
+      'template' => 'tripal_core_customize',
+      'path' => drupal_get_path('module', 'tripal_core') . '/theme'
     ),
   );
 }

tripal_cv/includes/tripal_cv_admin.inc

@@ -1,95 +1,4 @@
 <?php
-/**
- * Purpose: Provide Guidance to new Tripal Admin
- *
- * @return HTML Formatted text
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_module_description_page() {
-  $text = '';
-
-  $text = '<br><h3>Tripal Controlled Vocabulary Administrative Tools Quick Links</h3>';
-    $text .= '<ul>';
-      $text .= '<li>' . l('Add a Vocabulary', 'admin/tripal/tripal_cv/cv/add') . '</li>';
-      $text .= '<li>' . l('Edit a Vocabulary', 'admin/tripal/tripal_cv/cv/edit') . '</li>';
-      $text .= '<li>' . l('Load ontology with OBO file', 'admin/tripal/tripal_cv/obo_loader') . '</li>';
-      $text .= '<li>' . l('Add a Term', 'admin/tripal/tripal_cv/cvterm/add') . '</li>';
-      $text .= '<li>' . l('Edit a Term', 'admin/tripal/tripal_cv/cvterm/edit') . '</li>';      
-      $text .= '<li>' . l('Update cvtermpath', 'admin/tripal/tripal_cv/cvtermpath') . '</li>';
-    $text .= '</ul>';
-
-
-  $text .= '<h3>Module Description:</h3>';
-  $text .= '<p>The Tripal CV (Controlled Vocabularies) Module provides
-    functionality for managing controlled vocabularies and the terms they are
-    comprised of. The flexibility and extendibility of the chado schema depends
-    on controlled vocabularies. For example, by using a controlled vocabulary for
-    feature types the chado schema can describe features of any type, even those
-    we have not concieved of yet.</p>';
-
-  $text .= '<h3>Setup Instructions:</h3>';
-  $text .= '<p>After installation of the controlled vocabulary module, the following tasks should be performed:</p>';
-    $text .= '<ol>';
-      $text .= '<li><p><b>Set Permissions</b>: The cv module supports the Drupal user permissions interface for
-               controlling access to cv content and functions. These permissions include viewing,
-               creating, editing or administering of
-               cv content. The default is that only the original site administrator has these
-               permissions.  You can <a href="' . url('admin/user/roles') . '">add roles</a> for classifying users,
-               <a href="' . url('admin/user/user') . '">assign users to roles</a> and
-               <a href="' . url('admin/user/permissions') . '">assign permissions</a> for the cv content to
-               those roles.  For a simple setup, allow anonymous users access to view organism content and
-               allow the site administrator all other permissions.</p></li>';
-      $text .= '<li><b>Loading of Ontologies/Controlled Vocabularies</b>: You can access this loader at '.
-        l('Admin->Tripal Management->Tripal CV->Load Ontology With OBO File', 'admin/tripal/tripal_cv/obo_loader')
-        .'. This loader allows you to choose from a list of common ontologies or
-        enter the URL or location to an OBO file. Even the list of common
-        ontologies is using a URL ensuring you get the most up to date ontology.</p>';
-      $text .= '<p>This loader adds a Tripal Job which then waits in a queue to
-        be launched. To launch Tripal Jobs either navidate to the root of your
-        drupal installation and execute "php sites/all/modules/tripal/tripal_core/
-        tripal_launch_jobs.php <drupal user>" or set up a cron job (See user manual
-        for more details).</p>';
-      $text .= '<p>NOTE: in some cases, community developed ontologies for your
-        data may not yet be developed. In this case, it is suggested that you begin
-        developement of an ontology using one of the online tools. You might find
-        that many researchers are trying to deal with the same data and are willing
-        to help you in this endevor. You can ' . l('create a controlled vocabulary', 'admin/tripal/tripal_cv/add_cv') . ' and '
-        . l('add terms to it', 'admin/tripal/tripal_cv/add_cvterm')  . ' to provide functionality to your site while you are waiting
-        for the ontology to be developed.</p></li>';
-    $text .= '</ol>';
-
-  $text .= '<h3>Features of this Module:</h3>';
-  $text .= '<p>Aside from the data loading described above, the Tripal Controlled Vocabulary (CV) module also provides the following functionality:</p>';
-    $text .= '<ul>';
-      $text .= '<li><b>Create/Update/Delete A Controlled Vocaulbulary</b>: to create your own controlled vocabulary go to '.
-        l('Admin->Tripal Management->Tripal CV->Add a Controlled Vocabulary', 'admin/tripal/tripal_cv/add_cv')
-        .' and fill out the form provided.To Update/Delete a controlled vocabulary
-        go to ' . l('Admin->Tripal Management->Tripal CV->Update/Delete Controlled Vocabulary', 'admin/tripal/tripal_cv/edit_cv')
-        .', select the existing controlled vocabulary you want to modify and then
-        edit it as desired. This only modifies the name, description of a
-        controlled vocabulary. See the next section for adding, removing, editing
-        the term a controlled vocabulary contains.</li>';
-
-      $text .= '<li><b>Create a Controlled Vocaulbulary Term</b>: To Add a term to an already existing controlled vocabulary
-        go to ' . l('Admin->Tripal Management->Tripal CV->Add a Controlled Vocabulary Term', 'admin/tripal/tripal_cv/add_cvterm')
-        .', select the controlled vocabulary you want to add terms to and then fill
-        out the form.</li>';
-      $text .= '<li><b>Controlled Vocabulary Term Browser</b>: This module provides a ' . l('basic listing', 'admin/tripal/tripal_cv/list_cvterms') . ' of controlled vocabulry terms for
-              for all vocabularies currently in chado. It does not require indexing for Drupal searching but relies on Drupal Views.
-              <a href="http://drupal.org/project/views">Drupal Views</a> must be installed.</li>';
-      $text .= '<li><p><b>Integration with Drupal Views</b>: <a href="http://drupal.org/project/views">Drupal Views</a> is
-              a powerful tool that allows the site administrator to create lists or basic searching forms of Chado content.
-              It provides a graphical interface within Drupal to allow the site admin to directly query the Chado database
-              and create custom lists without PHP programming or customization of Tripal source code.  Views can also
-              be created to filter content that has not yet been synced with Druapl in order to protect access to non
-              published data (only works if Chado was installed using Tripal).  You can see a list of available pre-existing
-              Views <a href="' . url('admin/build/views/') . '">here</a>, as well as create your own. </p></li>';
-    $text .= '</ul>';
-
-  return $text;
-}
-
 /**
  * Purpose: Provides the form for Updating and Deleteing existing
  *   chado controlled vocabularies (See chado cv table)

tripal_cv/theme/tripal_cv_admin.tpl.php

@@ -0,0 +1,56 @@
+<br><h3>Tripal Controlled Vocabulary Administrative Tools Quick Links</h3>
+    <ul>
+      <li><?php print l('Add a Vocabulary', 'admin/tripal/tripal_cv/cv/add') ?></li>
+      <li><?php print l('Edit a Vocabulary', 'admin/tripal/tripal_cv/cv/edit') ?></li>
+      <li><?php print l('Load ontology with OBO file', 'admin/tripal/tripal_cv/obo_loader') ?></li>
+      <li><?php print l('Add a Term', 'admin/tripal/tripal_cv/cvterm/add') ?></li>
+      <li><?php print l('Edit a Term', 'admin/tripal/tripal_cv/cvterm/edit') ?></li>      
+      <li><?php print l('Update cvtermpath', 'admin/tripal/tripal_cv/cvtermpath') ?></li>
+    </ul>
+
+
+  <h3>Module Description:</h3>
+  <p>The Tripal CV (Controlled Vocabularies) Module provides
+    functionality for managing controlled vocabularies and the terms they are
+    comprised of. The flexibility and extendibility of the chado schema depends
+    on controlled vocabularies. For example, by using a controlled vocabulary for
+    feature types the chado schema can describe features of any type, even those
+    we have not concieved of yet.</p>
+
+  <h3>Setup Instructions:</h3>
+  <p>After installation of the controlled vocabulary module, the following tasks should be performed:</p>
+    <ol>
+        <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
+   or administer vocabularies and terms. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
+   permissions under the 'tripal_cv' section as appropriate for your site. For a simple setup, allow anonymous 
+   users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
+
+      <li><b>Loading of Ontologies/Controlled Vocabularies</b>: You can access this loader at <?php 
+        print l('Admin->Tripal Management->Tripal CV->Load Ontology With OBO File', 'admin/tripal/tripal_cv/obo_loader')
+        ?>. This loader allows you to choose from a list of common ontologies or
+        enter the URL or location to an OBO file. Even the list of common
+        ontologies is using a URL ensuring you get the most up to date ontology.</p>      
+      <p>NOTE: in some cases, community developed ontologies for your
+        data may not yet be developed. In this case, it is suggested that you begin
+        developement of an ontology using one of the online tools. You might find
+        that many researchers are trying to deal with the same data and are willing
+        to help you in this endevor. </p></li>
+    </ol>
+
+  <h3>Features of this Module:</h3>
+  <p>Aside from the data loading described above, the Tripal Controlled Vocabulary (CV) module also provides the following functionality:</p>
+    <ul>
+      <li><p><b>Create/Update/Delete A Controlled Vocaulbulary</b>: to create your own controlled vocabulary go to 
+        <?php l('the page for adding a vocbulary', 'admin/tripal/tripal_cv/cv/add') ?> and 
+        fill out the form provided. To Update/Delete a controlled vocabulary go to 
+        <?php print l('the page for editing a vocuabulary', 'admin/tripal/tripal_cv/cv/edit') ?>, 
+        select the existing vocabulary you want to modify and then
+        edit it as desired. This only modifies the vocabulary itself. See the next section for adding, removing, editing
+        the terms of a vocabulary.</p></li>
+
+      <li><p><b>Create a Controlled Vocaulbulary Term</b>: Use 
+        <?php print l('the page for adding a new CV term', 'admin/tripal/tripal_cv/cvterm/add') ?>, 
+        select the controlled vocabulary you want to add terms to and then fill
+        out the form.</p></li>      
+      
+    </ul>

tripal_cv/tripal_cv.module

@@ -44,8 +44,8 @@ function tripal_cv_menu() {
   $items['admin/tripal/tripal_cv'] = array(
     'title' => 'Vocabularies',
     'description' => 'Basic Description of Tripal CV Module Functionality',
-    'page callback' => 'tripal_cv_module_description_page',
-    'page arguments' => array(''),
+    'page callback' => 'theme',
+    'page arguments' => array('tripal_cv_admin'),
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_NORMAL_ITEM,
   );
@@ -235,4 +235,21 @@ function tripal_cv_form_alter(&$form, &$form_state, $form_id) {
       $form['#action'] = url("admin/tripal/tripal_cv/cvterm/add");
     }
   }
+}
+
+/**
+ *  We need to let drupal know about our theme functions and their arguments.
+ *  We create theme functions to allow users of the module to customize the
+ *  look and feel of the output generated in this module
+ *
+ * @ingroup tripal_db
+ */
+function tripal_cv_theme() {
+  return array(    
+    'tripal_cv_admin' => array(
+      'template' => 'tripal_cv_admin',  
+      'arguments' =>  array(NULL),  
+      'path' => drupal_get_path('module', 'tripal_cv') . '/theme', 
+    ),
+  );
 }

tripal_db/theme/tripal_db_admin.tpl.php

@@ -14,34 +14,21 @@
 
 <h3>Setup Instructions:</h3>
 <ol>
-<li><b>Set Permissions</b>: This module supports the Drupal user permissions interface for
-             controlling administrative access for creating, editing and deleting database cross-reference resources. 
-             The default is that only the site administrator has these
-             permissions.  Best practice is to create <a href="<?php print url('admin/user/roles') ?>">a new role</a> 
-             for administrative tasks, (such as a webmaster role),
-             and then <a href="<?php print url('admin/user/user') ?>">assign users to the role</a>. Finally,
-             <a href="<?php print url('admin/user/permissions') ?>">assign the permission</a> titled "administer db cross-reference".
-             to the new role.</li>
-<li><b>Adding or Editing an External Databases</b>. Many resources such as NCBI nr or ExPASy SwissProt (to name a few) 
+    <li><p><b>Set Permissions</b>: By default only the site administrator account has access to 
+   or administer databases. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
+   permissions under the 'tripal_db' section as appropriate for your site. For a simple setup, allow anonymous 
+   users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
+   
+<li><p><b>Adding or Editing an External Databases</b>. Many resources such as NCBI nr or ExPASy SwissProt (to name a few) 
           come pre-loaded with Chado.  However, you can add new entries or edit existing entries. Also, when loading 
           ontologies (controlled vocabularies) using the Tripal CV module new databases are added automaticaly for 
           each ontology.  To enable linking of accession on a page to the page for that accession on the external
-          database, simply add the URL and the URL prefix when adding or editing a database.</li>
+          database, simply add the URL and the URL prefix when adding or editing a database.</p></li>
 
-<li><b>Associate Data with Accessions</b>.  The Tripal loaders (e.g. GFF, OBO) can associate accessions from
+<li><p><b>Associate Data with Accessions</b>.  The Tripal loaders (e.g. GFF, OBO) can associate accessions from
           remote data to genomic features and controlled vocabularies automatically.  Use the loaders to load genomic
           features and controlled vocabularies respectively.  Additionally, the bulk loader can be used to create
           loading templates for associating external database accessions.  
-          </li>
+         </p></li>
 </ol>
 
-
-<br><h3>Features of this Module:</h3>
-<ul>
-<li><b>Add an External Databases</b>:
-By entering the name and any additional details into the <a href="tripal_db/add_db">add database form</a> you register an external database with your website. This allows you to specify that a sequence feature or other data is also stored in an external database. This is escpecially useful if the external database may contain additional details not stored in yours. If the external database is online you can even provide a URL prefix which will automatically link any data in your website to theirs via a web link.</li>
-
-<li><b>Update or Delete and External Databases</b>
-To edit the details of an external database record or to delete an already existing external database, go to the <a href="tripal_db/edit_db">Update/Delete DBs form</a>. This will allow you to change details or enter new details.</li>
-
-</ul>

tripal_feature/theme/tripal_feature_admin.tpl.php

@@ -8,33 +8,20 @@
  </ul>
 
   <h3>Module Description:</h3>
-  <p>This module provides an interface for the Chado feature module which stores information
-    related to genomic features.  This module provides support for bulk loading of data in
-    FASTA or GFF format, visualization of "feature" pages, editing and updating.
-    </p>
+  <p>The Tripal Feature module provides a new feature content type and interface for genomic features. </p>
 
   <h3>Setup Instructions:</h3>
   <p>After installation of the feature module.  The following tasks should be performed</p>
   <ol>
-    <li><p><b>Set Permissions</b>: The feature module supports the Drupal user permissions interface for
-     controlling access to feature content and functions. These permissions include viewing,
-     creating, editing or administering of
-     feature content. The default is that only the original site administrator has these
-     permissions.  You can <a href="<?php print url('admin/user/roles') ?>">add roles</a> for classifying users,
-     <a href="<?php print url('admin/user/user') ?>">assign users to roles</a> and
-     <a href="<?php print url('admin/user/permissions') ?>">assign permissions</a> for the feature content to
-     those roles.  For a simple setup, allow anonymous users access to view organism content and
-     allow the site administrator all other permissions.</p></li>
-
-     <li><p><b>Themeing</b>:  Before content from Chado can be visualized the Tripal base theme must
-     be installed.  This should have been done prior to this point.  But is mentioned here in the event you
-     follow the instructions below and cannot see content.  In this case, if you do not see content
-     check that Tripal theming is properly installed</p></li>
-
-     <li><p><b>Loading of Ontologies</b>:  If you
-     used Tripal to create the Chado database, then you must load ontologies before proceeding.  Visit the
-     page to <a href="<?php print url('admin/tripal/tripal_cv/obo_loader') ?>">load ontologies</a> and load at
-     least the following ontologies:
+    <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
+   or administer features. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
+   permissions under the 'tripal_feature' section as appropriate for your site. For a simple setup, allow anonymous 
+   users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
+   
+   <li><p><b>Loading of Ontologies</b>:  
+     Before loading genomic features you must also have several vocabularies loaded as well. Using the
+     <?php print l('OGO loader','admin/tripal/tripal_cv/obo_loader')?> you should load the following
+     ontologies:
      <ul>
         <li>Chado Feature Properties</li>
         <li>Relationship Ontology</li>
@@ -44,26 +31,29 @@
 
      <li><p><b>Create Organisms</b>:  Before adding feature data you must already have the
      organisms loaded in the database.  See the
-     <a href="<?php print url('admin/tripal/tripal_organism') ?>">Tripal Organism Admin page</a> for
+     <?php print l('Tripal Organism Admin Page','admin/tripal/tripal_organism') ?> for
      instructions for adding and Syncing organisms.</p></li>
 
-     <li><p><b>Create Analysis</b>:  Tripal requires that feature data loaded using the Tripal loaders
+     <li><p><b>Create an Analysis</b>:  Tripal requires that feature data loaded using the Tripal loaders
      be associated with an analyis.  This provides a grouping for the feature data and can be used
      later to visualize data pipelines.  Before loading feature data through the FASTA or GFF loaders
-     you will need to <a href="<?php print url('node/add') ?>">create an analysis</a> for the data.</p></li>
+     you will need to <?php print l('create an analysis','node/add/chado-analysis') ?> for the data.</p></li>
 
-     <li><p><b>Create Referring Database Entries</b>:  If you would like to associate your feature data with an
-     external reference database, check to ensure that the <a href="<?php print url('admin/tripal/tripal_db/edit_db') ?>">
-     database record already exists</a>.  If not you should <a href="<?php print url('admin/tripal/tripal_db/add_db') ?>">add a new database record</a> before importing
-     feature data.</p></li>
+     <li><p><b>Create Database Cross References</b>:  If you would like to associate your feature data with an
+     external database, check to ensure that the <?php print l('database already exists','admin/tripal/tripal_db/edit_db') ?>.
+     If not you should <?php print l('add a new database record','admin/tripal/tripal_db/add_db') ?> before importing
+     feature data. Be sure to set the URL and URL prefix for the database if you would like accessions (e.g. GO terms, NCBI
+     accession) to link out to the external database.</p></li>
 
      <li><p><b>Data Import</b>:  if you do not already have an existing Chado database with preloaded data
      then you will want
      to import data.  You can do so using the Chado perl scripts that come with the normal
-     <a href="http://gmod.org/wiki/Chado">distribution of Chado</a> or you can use the <a href="<?php print url('admin/tripal/tripal_feature/fasta_loader') ?>">FASTA loader</a> and
+     <a href="http://gmod.org/wiki/Chado">distribution of Chado</a> or you can use 
+     the <a href="<?php print url('admin/tripal/tripal_feature/fasta_loader') ?>">FASTA loader</a> and
      <a href="<?php print url('admin/tripal/tripal_feature/gff3_load') ?>">GFF loader</a> provided here.  If you
-     created the Chado database using Tripal then you\'ll most likely want to use the Tripal loaders.  If your data
-     is not condusive for loading with these loaders you may have to write your own loaders.
+     created the Chado database using Tripal then you'll most likely want to use the Tripal loaders.  If your data
+     is not condusive for loading with these loaders and you can get your data into a tab-delimited format you can
+     use Tripals' bulk loader.
      </p></li>
 
      <li><p><b>Sync Features</b>:  After data is loaded you need to sync features.  This process is what
@@ -81,21 +71,6 @@
      to specify whether to use the feature name, unique name or internal ID as the [feature] portion of the
      URL.  Select the one that will guarantee a unique identifier for feature pages.</p></li>
 
-     <li><p><b>Indexing</b>:  Once all data has been loaded (including analysis data--e.g. blast, interpro, etc.)
-     you can index all feature pages for searching if you want to ues the Drupal default search mechanism.
-     Use the <a href="<?php print url('admin/tripal/tripal_feature/configuration') ?>">Feature Configuration page</a>
-     to either Index (for the first time) or "Reindex" (after adding new data)
-     the feature pages for searching.  Once the site is 100% indexed the pages will be searchable using Drupal\'s
-     full text searching.  You can find the percent indexed for the entire site by visiting the
-     <a href="<?php print url('admin/settings/search') ?>">Search settings page</a>. Indexing
-     can take quite a while if you have a lot of data</p></li>
-
-     <li><p><b>Set Taxonomy</b>:  Drupal provides a mechanism for categorizing content to allow
-     for advanced searching.  Drupal calls this "Taxonomy", but is essentially categorizing the pages.
-     You can categorize feature pages by their type (e.g. gene, mRNA, contig, EST, etc.) and by the
-     organism to which they belong.  This allows for filtering of search results by organism and feature type.
-     Use the <a href="<?php print url('admin/tripal/tripal_feature/configuration') ?>">Feature Configuration page</a> to
-     set the Taxonomy.</p></li>
   </ol>
   </p>
 
@@ -125,66 +100,13 @@
     published data (only works if Chado was installed using Tripal).  You can see a list of available pre-existing
     Views <a href="<?php print url('admin/build/views/') ?>">here</a>, as well as create your own. </p></li>
 
-    <li><p><b>Basic Feature Lookup View</b>: This module provides a basic <a href="<?php print url('features') ?>">feature search
-    tool</a> for finding or listing features in Chado. It does not require indexing for Drupal searching but relies
-    on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a> must be installed. </p></li>
-
-    <li><p><b>Delete Features</b>: This module provides a <a href="<?php print url('admin/tripal/tripal_feature/delete') ?>">Delete Feature page</a>
-    for bulk deltions of features. You may delete features using a list of feature names, or for a specific organism
-    or for a specific feature type.</p></li>
+    <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/features') ?> is provided for 
+    finding features. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
+    which must be installed to see the search tool.  Look for it in the navigation menu under the item 
+    "Search Biological Data". </p></li>
 
+    <li><p><b>Delete Features</b>: You can  <a href="<?php print url('admin/tripal/tripal_feature/delete') ?>">bulk delete features</a>
+    by providing a list of feature names, or for a specific organism or for a specific feature type. Be sure you have
+    a full backup of your site before performing a bulk delete.</p></li>
   </ul>
-            </p>
-
-  <h3>Page Customizations</h3>
-  <p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
- Below is a description of several methods.  These methods may be used in conjunction with one another to
- provide fine-grained control.
- <ul>
-
- <li><p><b>Integration with Drupal Panels</b>:  <a href="http://drupal.org/project/views">Drupal Panels</a>
-  allows for customization of a page layout if you don\'t want to do PHP/Javascript/CSS programming.  Tripal comes with pre-set layouts for feature pages.  However,
-  Panels become useful if you prefer a layout that is different from the pre-set layouts.  Chado content
-  is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the
-  Panel\'s GUI.</p></li>
-
- <li><p><b>Drupal\'s Content Construction Kit (CCK)</b>: the
- <a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a> is a powerful way to add non-Chado content
- to any page without need to edit template files or knowing PHP.  You must first download and install CCK.
- With CCK, the site administartor can create a new field to appear on the page.  For example, currently,
- the Chado publication module is not yet supported by Tripal.  Therefore, the site administrator can add a text
- field to the feature pages.  This content is not stored in Chado, but will appear on the feature page.  A field
- added by CCK will also appear in the form when editing a feature to allow users to manually enter the appropriate
- text.  If the default pre-set layout and themeing for Tripal is used, it is better to create the CCK element,
- indicate that it is not to be shown (using the CCK interface), then manually add the new content type
- where desired by editing the templates (as described below).  If using Panels, the CCK field can be added to the
- location desired using the Panels interface.</p></li>
-
- <li><p><b>Drupal Node Templates</b>:  The Tripal packages comes with a "theme_tripal" directory that contains the
- themeing for Chado content.    The feature module has a template file for feature "nodes" (Tripal feature pages).  This file
- is named "node-chado_feature.tpl.php", and provides javascript, HTML and PHP code for display of the feature
- pages.  You can edit this file to control which types of information (or which feature "blocks") are displayed for features. Be sure to
- copy these template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
- future Tripal updates may overwrite your customizations. See the <a href="http://tripal.info/">Tripal website </a>
- for instructions on how to access variables and other Chado content within the template file.</p></li>
-
- <li><p><b>Feature "Block" Templates</b>:  In the "theme_tripal" directory is a subdirectory named "tripal_feature".
- Inside this directory is a set of templates that control distinct types of information for features.  For example,
- there is a "base" template for displaying of data directly from the Chado feature table, and a "references"
- template for showing external site references for a feature (data from the feature_dbxref table).  These templates are used both by Drupal blocks
- for use in Drupal Panels (as described above) or for use in the default pre-set layout that the node template
- provides (also desribed above).  You can customize this template as you desire.  Be sure to copy the
- template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
- future Tripal updates may overwrite your customizations.  See the <a href="http://tripal.info/">Tripal website </a>
- for instructions on how to access variables and other Chado content within the template files.</p></li>
- </li>
-
- <li><p><b>Adding Links to the "Resources" Sidebar</b>: If you use the pre-set default Tripal layout for theming, you
- will see a "Resources" sidebar on each page.  The links that appear on the sidebar are automatically generated
- using Javascript for all of the feature "Blocks" that appear on the page. If you want to add additional links
- (e.g. a dynamic link to GBrowse for the feature) and you want that link to appear in the
- "Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the
- section at the bottom of the template file where the resources section is found.</p></li>
-
- </ul>
- </p>
+</p>

tripal_featuremap/theme/tripal_featuremap_admin.tpl.php

@@ -11,41 +11,31 @@
 
 <h3>Setup Instructions:</h3>
 <ol>
-  <li><p>
-    <b>Set Permissions</b>: The map module supports the Drupal user permissions interface for
-    controlling access to map content and functions. These permissions include viewing,
-    creating, editing or administering of
-    map content. The default is that only the  site administrator has these
-    permissions.  You can <a href="<?php print url('admin/user/roles') ?>">add roles</a> for classifying users,
-    <a href="<?php print url('admin/user/user') ?>">assign users to roles</a> and
-    <a href="<?php print url('admin/user/permissions') ?>">assign permissions</a> for the map content to
-    those roles.  For a simple setup, allow anonymous users access to view map content and
-    allow the site administrator all other permissions.
-  </p></li>  
+   <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
+   or administer features. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
+   permissions under the 'tripal_library' section as appropriate for your site. For a simple setup, allow anonymous 
+   users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
+ 
+ <li><p><b>Create a Map</b>:  An map (called a feature map in Chado) can be <?php print l('created', 'node/add/chado-featuremap')?> 
+ manually in the same way any other data type.  There is no loader for loading large files of map information including
+ features that may be associated with these maps (e.g. genetic markers).  The Tripal bulk loader is the only way
+ to load this type of data.</p></li>
+ 
+ <li><p><b>Sync any Existing Maps</b>: Before Maps can be viewed on the website, they must first be <?php print l('created manually', 'node/add/chado-featuremap')  ?> 
+          or if they already exist in the Chado database they must be synced. Near the top of the <?php print l('Map Configuration page', 'admin/tripal/tripal_featuremap/configuration') ?>
+          there is
+          a Sync Maps section which provides list of maps currently in chado which can be sync\'d.
+          Simply select the maps you would like to create Drupal/Tripal pages for and click Sync Maps. Once synced, 
+          pages will appear on the site for maps.</p></li>
+ 
 </ol>
 
 
 <h3>Features of this Module:</h3>
 <ul>
-  <li><p><b>Add a map</b>: Maps can be manually created <?php  print l('here', 'node/add/chado-featuremap') ?></p></li>
   <li><p><b>Edit or Delete Maps</b>: Maps can be manually edited or deleted by navigating to the map page and clicking the "Edit" button.</p></li>  
-  <li><p><b>Sync any Existing Maps</b>: Before Maps can be viewed on the website, they must first be <?php print l('created manually', 'node/add/chado-featuremap')  ?> 
-            or if they already exist in the Chado database they must be synced. Near the top of the <?php print l('Map Configuration page', 'admin/tripal/tripal_featuremap/configuration') ?>
-            there is
-            a Sync Maps section which provides list of maps currently in chado which can be sync\'d.
-            Simply select the maps you would like to create Drupal/Tripal pages for and click Sync Maps. Once synced, 
-            pages will appear on the site for maps.</p></li>
-  <li><p><b>Integration with Drupal Views</b>: <a href="http://drupal.org/project/views">Drupal Views</a> is
-            a powerful tool that allows the site administrator to create lists or basic search forms of Chado content.
-            It provides a graphical interface within Drupal to allow the site admin to directly query the Chado database
-            and create custom lists without PHP programming or customization of Tripal source code.  Views can also
-            be created to filter out records that has not yet been synced with Drupal in order to protect access to non
-            published data (only works if Chado was installed using Tripal).  You can see a list of available pre-existing
-            Views <a href="<?php print url('admin/build/views/') ?>">here</a>, as well as create your own. </p></li>
-</ul>
-
-<h3>Page Customizations</h3>
-<p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
-   See the <a href="http://www.gmod.org/wiki/Tripal_Developer's_Handbook">Developers Handbook</a> for further infromation 
-   to customize Map pages.
-</p>
+    <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/featuremaps') ?> is provided for 
+    finding maps. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
+    which must be installed to see the search tool.  Look for it in the navigation menu under the item 
+    "Search Biological Data". </p></li>
+</ul>

tripal_genetic/tripal_genetic.module

@@ -44,9 +44,16 @@ function tripal_genetic_nodeapi(&$node, $op, $teaser, $page) {
   switch ($op) {
     case 'view':
       if ($node->type == 'chado_feature') {
-        $node->content['tripal_feature_genotypes'] = array(
-          '#value' => theme('tripal_feature_genotypes', $node),
-        );
+        // the tripal_natural_diversity module provides a tripal_feature_nd_genotype
+        // template.  The only difference between them is the addition of 
+        // project information by this ND module's template.  Therefore,
+        // if the tripal_natural_diversity content is present then don't add the
+        // template from this module as the ND module would superceed this.
+        if (!array_key_exists('tripal_feature_nd_genotypes', $node->content)) {
+          $node->content['tripal_feature_genotypes'] = array(
+            '#value' => theme('tripal_feature_genotypes', $node),
+          );
+        }
       }
   }
 }

tripal_library/theme/tripal_library_admin.tpl.php

@@ -8,87 +8,25 @@
 
 <h3>Setup Instructions:</h3>
 <ol>
-<li><p><b>Set Permissions</b>: The library module supports the Drupal user permissions interface for
-   controlling access to library content and functions. These permissions include viewing,
-   creating, editing or administering of
-   library content. The default is that only the original site administrator has these
-   permissions.  You can <a href="<?php print url('admin/user/roles') ?>">add roles</a> for classifying users,
-   <a href="<?php print url('admin/user/user') ?>">assign users to roles</a> and
-   <a href="<?php print url('admin/user/permissions') ?>">assign permissions</a> for the library content to
-   those roles.  For a simple setup, allow anonymous users access to view organism content and
-   allow the site administrator all other permissions.</p></li>
-<li><p><b>Sync any Existing Libraries</b>: Near the top of the ' . l('Library Configuration page', 'admin/tripal/tripal_library/configuration') ?> there is
-  a Sync Libraries section which provides list of libraries currently in chado which can be sync\'d.
+  <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
+   or administer features. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
+   permissions under the 'tripal_library' section as appropriate for your site. For a simple setup, allow anonymous 
+   users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
+
+<li><p><b>Sync any Existing Libraries</b>: Near the top of the <?php  l('Library Configuration page', 'admin/tripal/tripal_library/configuration') ?> there is
+  a Sync Libraries section which provides list of libraries currently in chado which can be synced.
   Simply select the libraries you would like to create Drupal/Tripal pages for and click Sync Libraries.</p></li>
 </ol>
 
 
 <h3>Features of this Module:</h3>
 <ul>
-  <li><b>Add/Edit/Delete Libraries</b>: Libraries with no associated features can be created ' . l('here', 'node/add/chado-library') ?> but it is
-  recommended to create the library using the feature loader. For example, when you load FASTA files using the Tripal loader you are
-  given the option of specifying a library for all created features. Existing Libraries (regardless of the method used to create them) can be
+  <li><b>Add/Edit/Delete Libraries</b>: Libraries with no associated features can be created <?php print l('here', 'node/add/chado-library') ?>.  
+  Existing Libraries (regardless of the method used to create them) can be
   edited or deleted by clicking the Edit tab at the top of the Library Page.</li>
-  <li><p><b>Integration with Drupal Views</b>: <a href="http://drupal.org/project/views">Drupal Views</a> is
-  a powerful tool that allows the site administrator to create lists or basic searching forms of Chado content.
-  It provides a graphical interface within Drupal to allow the site admin to directly query the Chado database
-  and create custom lists without PHP programming or customization of Tripal source code.  Views can also
-  be created to filter content that has not yet been synced with Druapl in order to protect access to non
-  published data (only works if Chado was installed using Tripal).  You can see a list of available pre-existing
-  Views <a href="<?php print url('admin/build/views/') ?>">here</a>, as well as create your own. </p></li>
-  <li><b>Basic Listing</b>: This module provides a basic <a href="<?php print url('libraries') ?>">library display
-  tool</a> for finding or listing libraries in Chado. It does not require indexing for Drupal searching but relies
-  on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a> must be installed.</li>
-</ul>
-
-<h3>Page Customizations</h3>
-<p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
-Below is a description of several methods.  These methods may be used in conjunction with one another to
-provide fine-grained control.
-<ul>
-
-<li><p><b>Integration with Drupal Panels</b>:  <a href="http://drupal.org/project/views">Drupal Panels</a>
-allows for customization of a page layout if you don\'t want to do PHP/Javascript/CSS programming.  Tripal comes with pre-set layouts for library pages.  However,
-Panels become useful if you prefer a layout that is different from the pre-set layouts.  Chado content
-is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the
-Panel\'s GUI.</p></li>
-
-<li><p><b>Drupal\'s Content Construction Kit (CCK)</b>: the
-<a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a> is a powerful way to add non-Chado content
-to any page without need to edit template files or knowing PHP.  You must first download and install CCK.
-With CCK, the site administartor can create a new field to appear on the page.  For example, currently,
-the Chado publication module is not yet supported by Tripal.  Therefore, the site administrator can add a text
-field to the library pages.  This content is not stored in Chado, but will appear on the library page.  A field
-added by CCK will also appear in the form when editing a library to allow users to manually enter the appropriate
-text.  If the default pre-set layout and themeing for Tripal is used, it is better to create the CCK element,
-indicate that it is not to be shown (using the CCK interface), then manually add the new content type
-where desired by editing the templates (as described below).  If using Panels, the CCK field can be added to the
-location desired using the Panels interface.</p></li>
-
-<li><p><b>Drupal Node Templates</b>:  The Tripal packages comes with a "theme_tripal" directory that contains the
-themeing for Chado content.    The library module has a template file for library "nodes" (Tripal library pages).  This file
-is named "node-chado_library.tpl.php", and provides javascript, HTML and PHP code for display of the library
-pages.  You can edit this file to control which types of information (or which library "blocks") are displayed for libraries. Be sure to
-copy these template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
-future Tripal updates may overwrite your customizations. See the <a href="http://tripal.info">Tripal website </a>
-for instructions on how to access variables and other Chado content within the template file.</p></li>
-
-<li><p><b>Library "Block" Templates</b>:  In the "theme_tripal" directory is a subdirectory named "tripal_library".
-Inside this directory is a set of templates that control distinct types of information for libraries.  For example,
-there is a "base" template for displaying of data directly from the Chado library table.  These templates are used both by Drupal blocks
-for use in Drupal Panels (as described above) or for use in the default pre-set layout that the node template
-provides (also desribed above).  You can customize this template as you desire.  Be sure to copy the
-template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
-future Tripal updates may overwrite your customizations.  See the <a href="http://tripal.info">Tripal website </a>
-for instructions on how to access variables and other Chado content within the template files.</p></li>
-</li>
-
-<li><p><b>Adding Links to the "Resources" Sidebar</b>: If you use the pre-set default Tripal layout for theming, you
-will see a "Resources" sidebar on each page.  The links that appear on the sidebar are automatically generated
-using Javascript for all of the library "Blocks" that appear on the page. If you want to add additional links
-(e.g. a link to a views table showing all features of the current library) and you want that link to appear in the
-"Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the
-section at the bottom of the template file where the resources section is found.</p></li>
-
+  
+    <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/libraries') ?> is provided for 
+    finding libraries. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
+    which must be installed to see the search tool.  Look for it in the navigation menu under the item 
+    "Search Biological Data". </p></li>
 </ul>
-</p>

tripal_natural_diversity/tripal_natural_diversity.module

@@ -51,10 +51,18 @@ function tripal_natural_diversity_theme() {
 /*
  *
  */
-function tripal_natural_diversity_nodeapi(&$node, $op, $teaser, $page){
+function tripal_natural_diversity_nodeapi(&$node, $op, $teaser, $page){  
   switch ($op) {
     case 'view':
       if ($node->type == 'chado_feature') {
+        // the tripal_genetic module provides a tripal_feature_genotype
+        // template.  The only difference between them is the addition of 
+        // project information by this module's template.  Therefore,
+        // if the tripal_genetic content is present get rid of as this
+        // module superceeds it.
+        if (array_key_exists('tripal_feature_genotypes', $node->content)) {
+          unset($node->content['tripal_feature_genotypes']);
+        }
         $node->content['tripal_feature_nd_genotypes'] = array(
            '#value' => theme('tripal_feature_nd_genotypes', $node),
         );

tripal_organism/theme/tripal_organism_admin.tpl.php

@@ -15,17 +15,12 @@
   <h3>Setup Instructions:</h3>
   <p>After installation of the organism module.  The following tasks should be performed.
             <ol>
-              <li><p><b>Set Permissions</b>: The organism module supports the Drupal user permissions interface for
-               controlling access to organism content and functions. These permissions include viewing,
-               creating, editing or administering of
-               organism content. The default is that only the original site administrator has these
-               permissions.  You can <a href="<?php print url('admin/user/roles') ?>">add roles</a> for classifying users,
-               <a href="<?php print url('admin/user/user') ?>">assign users to roles</a> and
-               <a href="<?php print url('admin/user/permissions') ?>">assign permissions</a> for the organism content to
-               those roles. For a simple setup, allow anonymous users access to view organism content and
-               allow the site administrator all other permissions.</p></li>
+                <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
+   or administer features. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
+   permissions under the 'tripal_organism' section as appropriate for your site. For a simple setup, allow anonymous 
+   users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
 
-              <li><p><b>Create Organisms</b>: Organism pages can be created in two ways:
+              <li><p><b>Create an Organism</b>: Organism pages can be created in two ways:
                  <ol>
                   <li><b>Sync Organisms</b>: If your organism has been pre-loaded into Chado then you need to sync the organism.
                    This process is what creates the pages for viewing online.  Not all organisms need be synced, only those
@@ -37,91 +32,16 @@
                    Once saved, the organism will be present in Chado and also "synced".
                  </ol></p></li>
 
-               <li><p><b>Indexing</b>:  Once organism pages are ready for public access,
-               you can index the organism pages for searching if you want to ues the Drupal default search mechanism.
-               Use the <a href="<?php print url('admin/tripal/tripal_organism/configuration') ?>">Organism Configuration page</a>
-               to either Index (for the first time) or "Reindex" (after updating data)
-               the organism pages for searching.  Once the site is 100% indexed the pages will be searchable using Drupal\'s
-               full text searching.  You can find the percent indexed for the entire site by visiting the
-               <a href="<?php print url('admin/settings/search') ?>">Search settings page</a>. Indexing
-               can take quite a while if you have a lot of data</p></li>
-
-               <li><p><b>Set Taxonomy</b>:  Drupal provides a mechanism for categorizing content to allow
-               for advanced searching.  Drupal calls this "Taxonomy", but is essentially categorizing the pages.
-               You can categorize feature pages by the
-               organism to which they belong.  This allows for filtering of search results by organism.
-               Use the <a href="<?php print url('admin/tripal/tripal_organism/configuration') ?>">Organism Configuration page</a> to
-               set the Taxonomy.</p></li>
              </ol>
 
   <h3>Features of this Module:</h3>
   <p>Aside from organism page setup (as described in the Setup section above),
             The Tripal organism module also provides the following functionality
             <ul>
-              <li><p><b>Integration with Drupal Views</b>: <a href="http://drupal.org/project/views">Drupal Views</a> is
-              a powerful tool that allows the site administrator to create lists or basic searching forms of Chado content.
-              It provides a graphical interface within Drupal to allow the site admin to directly query the Chado database
-              and create custom lists without PHP programming or customization of Tripal source code.  Views can also
-              be created to filter content that has not yet been synced with Druapl in order to protect access to non
-              published data (only works if Chado was installed using Tripal).  You can see a list of available pre-existing
-              Views <a href="<?php print url('admin/build/views/') ?>">here</a>, as well as create your own. </p></li>
 
-              <li><p><b>Basic Organism List</b>: This module provides a basic <a href="<?php print url('organisms') ?>">organism list</a>
-              for showing the list of organisms in Chado. <a href="http://drupal.org/project/views">Drupal Views</a> must be
-              installed. You can use the Views interface to alter the appearance of this list.</p></li>
+    <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/organisms') ?> is provided for 
+    finding organisms. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
+    which must be installed to see the search tool.  Look for it in the navigation menu under the item 
+    "Search Biological Data". </p></li>
             </ul>
             </p>
-
-  <h3>Page Customizations</h3>
-  <p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
-             Below is a description of several methods.  These methods may be used in conjunction with one another to
-             provide fine-grained control.
-             <ul>
-
-             <li><p><b>Integration with Drupal Panels</b>:  <a href="http://drupal.org/project/views">Drupal Panels</a>
-              allows for customization of a page layout if you don\'t want to do PHP/Javascript/CSS programming.  Tripal comes with pre-set layouts for organism pages.  However,
-              Panels become useful if you prefer a layout that is different from the pre-set layouts.  Chado content
-              is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the
-              Panel\'s GUI.</p></li>
-
-             <li><p><b>Drupal\'s Content Construction Kit (CCK)</b>: the
-             <a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a> is a powerful way to add non-Chado content
-             to any page without need to edit template files or knowing PHP.  You must first download and install CCK.
-             With CCK, the site administartor can create a new field to appear on the page.  For example, currently,
-             the Chado publication module is not yet supported by Tripal.  Therefore, the site administrator can add a text
-             field to the organism pages.  This content is not stored in Chado, but will appear on the organism page.  A field
-             added by CCK will also appear in the form when editing a organism to allow users to manually enter the appropriate
-             text.  If the default pre-set layout and themeing for Tripal is used, it is better to create the CCK element,
-             indicate that it is not to be shown (using the CCK interface), then manually add the new content type
-             where desired by editing the templates (as described below).  If using Panels, the CCK field can be added to the
-             location desired using the Panels interface.</p></li>
-
-             <li><p><b>Drupal Node Templates</b>:  The Tripal packages comes with a "theme_tripal" directory that contains the
-             themeing for Chado content.    The organism module has a template file for organism "nodes" (Tripal organism pages).  This file
-             is named "node-chado_organism.tpl.php", and provides javascript, HTML and PHP code for display of the organism
-             pages.  You can edit this file to control which types of information (or which organism "blocks") are displayed for organisms. Be sure to
-             copy these template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
-             future Tripal updates may overwrite your customizations. See the <a href="http://tripal.info/">Tripal website </a>
-             for instructions on how to access variables and other Chado content within the template file.</p></li>
-
-             <li><p><b>Organism "Block" Templates</b>:  In the "theme_tripal" directory is a subdirectory named "tripal_organism".
-             Inside this directory is a set of templates that control distinct types of information for organisms.  For example,
-             there is a "base" template for displaying of data directly from the Chado organism table, and a "references"
-             template for showing external site references for a organism (data from the organism_dbxref table).  These templates are used both by Drupal blocks
-             for use in Drupal Panels (as described above) or for use in the default pre-set layout that the node template
-             provides (also desribed above).  You can customize this template as you desire.  Be sure to copy the
-             template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
-             future Tripal updates may overwrite your customizations.  See the <a href="http://tripal.info/">Tripal website </a>
-             for instructions on how to access variables and other Chado content within the template files.</p></li>
-             </li>
-
-             <li><p><b>Adding Links to the "Resources" Sidebar</b>: If you use the pre-set default Tripal layout for theming, you
-             will see a "Resources" sidebar on each page.  The links that appear on the sidebar are automatically generated
-             using Javascript for all of the organism "Blocks" that appear on the page. If you want to add additional links
-             (e.g. a dynamic link to GBrowse for the organism) and you want that link to appear in the
-             "Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the
-             section at the bottom of the template file where the resources section is found.</p></li>
-
-             </ul>
-             </p>
-  

tripal_project/theme/tripal_project_admin.tpl.php

@@ -7,16 +7,12 @@
 
 <h3>Setup Instructions:</h3>
 <ol>
-<li><p><b>Set Permissions</b>: The project module supports the Drupal user permissions interface for
-   controlling access to project content and functions. These permissions include viewing,
-   creating, editing or administering of
-   project content. The default is that only the original site administrator has these
-   permissions.  You can <a href="<?php print url('admin/user/roles') ?>">add roles</a> for classifying users,
-   <a href="<?php print url('admin/user/user') ?>">assign users to roles</a> and
-   <a href="<?php print url('admin/user/permissions') ?>">assign permissions</a> for the project content to
-   those roles.  For a simple setup, allow anonymous users access to view organism content and
-   allow the site administrator all other permissions.</p></li>
-<li><p><b>Sync any Existing Projects</b>: Near the top of the ' . l('Project Configuration page', 'admin/tripal/tripal_project/configuration') ?> there is
+   <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
+   or administer features. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
+   permissions under the 'tripal_project' section as appropriate for your site. For a simple setup, allow anonymous 
+   users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
+
+<li><p><b>Sync any Existing Projects</b>: Near the top of the <?php print l('Project Configuration page', 'admin/tripal/tripal_project/configuration') ?> there is
   a Sync Projects section which provides list of projects currently in chado which can be sync\'d.
   Simply select the projects you would like to create Drupal/Tripal pages for and click Sync Projects.</p></li>
 </ol>
@@ -24,70 +20,12 @@
 
 <h3>Features of this Module:</h3>
 <ul>
-  <li><b>Add/Edit/Delete Projects</b>: Projects with no associated features can be created ' . l('here', 'node/add/chado-project') ?> but it is
-  recommended to create the project using the feature loader. For example, when you load FASTA files using the Tripal loader you are
-  given the option of specifying a project for all created features. Existing Projects (regardless of the method used to create them) can be
+  <li><b>Add/Edit/Delete Projects</b>: Projects can be created ' . l('here', 'node/add/chado-project') ?>. 
+  After creation, projects (regardless of the method used to create them) can be
   edited or deleted by clicking the Edit tab at the top of the Project Page.</li>
-  <li><p><b>Integration with Drupal Views</b>: <a href="http://drupal.org/project/views">Drupal Views</a> is
-  a powerful tool that allows the site administrator to create lists or basic searching forms of Chado content.
-  It provides a graphical interface within Drupal to allow the site admin to directly query the Chado database
-  and create custom lists without PHP programming or customization of Tripal source code.  Views can also
-  be created to filter content that has not yet been synced with Druapl in order to protect access to non
-  published data (only works if Chado was installed using Tripal).  You can see a list of available pre-existing
-  Views <a href="<?php print url('admin/build/views/') ?>">here</a>, as well as create your own. </p></li>
-  <li><b>Basic Listing</b>: This module provides a basic <a href="<?php print url('projects') ?>">project display
-  tool</a> for finding or listing projects in Chado. It does not require indexing for Drupal searching but relies
-  on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a> must be installed.</li>
-</ul>
-
-<h3>Page Customizations</h3>
-<p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
-Below is a description of several methods.  These methods may be used in conjunction with one another to
-provide fine-grained control.
-<ul>
-
-<li><p><b>Integration with Drupal Panels</b>:  <a href="http://drupal.org/project/views">Drupal Panels</a>
-allows for customization of a page layout if you don\'t want to do PHP/Javascript/CSS programming.  Tripal comes with pre-set layouts for project pages.  However,
-Panels become useful if you prefer a layout that is different from the pre-set layouts.  Chado content
-is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the
-Panel\'s GUI.</p></li>
+    <li><p><b>Simple Search Tool</b>: A <?php print l('simple search tool','chado/projects') ?> is provided for 
+    finding projects. This tool relies on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a>
+    which must be installed to see the search tool.  Look for it in the navigation menu under the item 
+    "Search Biological Data". </p></li>
 
-<li><p><b>Drupal\'s Content Construction Kit (CCK)</b>: the
-<a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a> is a powerful way to add non-Chado content
-to any page without need to edit template files or knowing PHP.  You must first download and install CCK.
-With CCK, the site administartor can create a new field to appear on the page.  For example, currently,
-the Chado publication module is not yet supported by Tripal.  Therefore, the site administrator can add a text
-field to the project pages.  This content is not stored in Chado, but will appear on the project page.  A field
-added by CCK will also appear in the form when editing a project to allow users to manually enter the appropriate
-text.  If the default pre-set layout and themeing for Tripal is used, it is better to create the CCK element,
-indicate that it is not to be shown (using the CCK interface), then manually add the new content type
-where desired by editing the templates (as described below).  If using Panels, the CCK field can be added to the
-location desired using the Panels interface.</p></li>
-
-<li><p><b>Drupal Node Templates</b>:  The Tripal packages comes with a "theme_tripal" directory that contains the
-themeing for Chado content.    The project module has a template file for project "nodes" (Tripal project pages).  This file
-is named "node-chado_project.tpl.php", and provides javascript, HTML and PHP code for display of the project
-pages.  You can edit this file to control which types of information (or which project "blocks") are displayed for projects. Be sure to
-copy these template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
-future Tripal updates may overwrite your customizations. See the <a href="http://tripal.info">Tripal website </a>
-for instructions on how to access variables and other Chado content within the template file.</p></li>
-
-<li><p><b>Project "Block" Templates</b>:  In the "theme_tripal" directory is a subdirectory named "tripal_project".
-Inside this directory is a set of templates that control distinct types of information for projects.  For example,
-there is a "base" template for displaying of data directly from the Chado project table.  These templates are used both by Drupal blocks
-for use in Drupal Panels (as described above) or for use in the default pre-set layout that the node template
-provides (also desribed above).  You can customize this template as you desire.  Be sure to copy the
-template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
-future Tripal updates may overwrite your customizations.  See the <a href="http://tripal.info">Tripal website </a>
-for instructions on how to access variables and other Chado content within the template files.</p></li>
-</li>
-
-<li><p><b>Adding Links to the "Resources" Sidebar</b>: If you use the pre-set default Tripal layout for theming, you
-will see a "Resources" sidebar on each page.  The links that appear on the sidebar are automatically generated
-using Javascript for all of the project "Blocks" that appear on the page. If you want to add additional links
-(e.g. a link to a views table showing all features of the current project) and you want that link to appear in the
-"Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the
-section at the bottom of the template file where the resources section is found.</p></li>
-
-</ul>
-</p>
+</ul>

tripal_stock/theme/tripal_stock_admin.tpl.php

@@ -9,6 +9,11 @@
 
   <h3>Setup Instructions:</h3>
   <ol>
+ <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
+   or administer analyses. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
+   permissions under the 'tripal_stock' section as appropriate for your site. For a simple setup, allow anonymous 
+   users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
+
   <li><b>Set Ontologies</b>: Since at the time of this modules developement there is no accepted ontology for
             describing stocks, their properties and relationships, this module allows you to select the controlled
             vocabularies (CVs) in your Chado Database you would like to govern these data. To Set the Controlled Vocabularies for Stocks:
@@ -53,63 +58,3 @@
   <p>The Stock Details Page also acts as a landing pad for updating/deleting stocks. To <b>update a stock</b>, go to the stocks details page and click on the Edit tab near the top of the page. This tab will only be visable if you have permission to edit chado stock content (See post installation steps above for information on setting user permissions). If you want to <b>delete a stock</b>, click the Edit tab and then near the bottom of the form, click the Delete button. This will delete the entire stock including it's properties, database references and any relationships including it.</p>
   <p>To <b>update/delete a given property of a stock</b>, click the "Edit Properties" Tab near the top of the stock details page. This form provides a listing of all existing properties for the given stock with form elements allowing you to change their value. After editing the properties you wanted to, simply click the "Update Properties" button to update all the properties for that stock. To delete a given property simply click the "Delete" Button beside the property you want to delete. You cannot undo this action! To <b>add a property to the given stock</b> simply fill out the "Add Property" form at the bottom of the "Edit Properties" Tab.</p>
   <p><b>Adding, updating and deleting Database References and Relationships</b> for a given stock is exactly the same as the method for properties. To edit Database References, click the "Edit DB References" tab and to add/edit/update stock relationships, click the "Edit Relationships" tab.</p></li>
-
-  <li><b><a href="../../stocks">Basic Listing of Stocks:</a></b>
-  <p>This module also provides a basic listing of all stocks currently sync'd with Drupal. To access this listing, there should be a Stocks Primary Menu item which links you to <a href="../../stocks">this page</a>. This page lists each stock on it's own row and provides a link to each stock by clicking on it's name. Currently there is no way to easily customize this listing.</p></li>
-
-  <li><b><a href="../build/views/">Flexible Listing of Stocks using Drupal Views:</a></b>
-  <p>In order to access a more flexible listing of stocks you must first install the <a href="http://drupal.org/project/views">Drupal Views2 module</a>. You should then be able to access the default views <a href="../build/views/">here</a>. Essentially, Views is a module which allows you to create custom SQL queries completely through the web interface without knowing SQL. Furthermore, it also does some formatting of the results allowing you to display them as HTML lists, tables or grids. You can also expose filters to the user to let them customize the results they see and even implement various sorting.</p>
-  <p>To use one of the Default Views simply click "Enable" and then "Edit" to change it to show exactly what you want. To view the current listing simply clikc "View Page" at the top of the Edit user interface. There are a number of good tutorials out there for Views2, any of which can be used to help you create your own custom listings of biological content. (Note: there aren't any tutorials specifically for tripal content but any tutorial for Views2 will show you how to use the views interface.</p></li>
-
-  <h3>Page Customizations</h3>
-  <p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
-     Below is a description of several methods.  These methods may be used in conjunction with one another to
-     provide fine-grained control.
-     <ul>
-
-     <li><p><b>Integration with Drupal Panels</b>:  <a href="http://drupal.org/project/views">Drupal Panels</a>
-      allows for customization of a page layout if you don't want to do PHP/Javascript/CSS programming.  Tripal comes with pre-set layouts for stock pages.  However,
-      Panels become useful if you prefer a layout that is different from the pre-set layouts.  Chado content
-      is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the
-      Panel's GUI.</p></li>
-
-     <li><p><b>Drupal's Content Construction Kit (CCK)</b>: the
-     <a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a> is a powerful way to add non-Chado content
-     to any page without need to edit template files or knowing PHP.  You must first download and install CCK.
-     With CCK, the site administartor can create a new field to appear on the page.  For example, currently,
-     the Chado publication module is not yet supported by Tripal.  Therefore, the site administrator can add a text
-     field to the stock pages.  This content is not stored in Chado, but will appear on the stock page.  A field
-     added by CCK will also appear in the form when editing a stock to allow users to manually enter the appropriate
-     text.  If the default pre-set layout and themeing for Tripal is used, it is better to create the CCK element,
-     indicate that it is not to be shown (using the CCK interface), then manually add the new content type
-     where desired by editing the templates (as described below).  If using Panels, the CCK field can be added to the
-     location desired using the Panels interface.</p></li>
-
-     <li><p><b>Drupal Node Templates</b>:  The Tripal packages comes with a "theme_tripal" directory that contains the
-     themeing for Chado content.    The stock module has a template file for stock "nodes" (Tripal stock pages).  This file
-     is named "node-chado_stock.tpl.php", and provides javascript, HTML and PHP code for display of the stock
-     pages.  You can edit this file to control which types of information (or which stock "blocks") are displayed for stocks. Be sure to
-     copy these template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
-     future Tripal updates may overwrite your customizations. See the <a href="http://tripal.info/">Tripal website </a>
-     for instructions on how to access variables and other Chado content within the template file.</p></li>
-
-     <li><p><b>Stock "Block" Templates</b>:  In the "theme_tripal" directory is a subdirectory named "tripal_stock".
-     Inside this directory is a set of templates that control distinct types of information for stocks.  For example,
-     there is a "base" template for displaying of data directly from the Chado stock table, and a "references"
-     template for showing external site references for a stock (data from the stock_dbxref table).  These templates are used both by Drupal blocks
-     for use in Drupal Panels (as described above) or for use in the default pre-set layout that the node template
-     provides (also desribed above).  You can customize this template as you desire.  Be sure to copy the
-     template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
-     future Tripal updates may overwrite your customizations.  See the <a href="http://tripal.info/">Tripal website </a>
-     for instructions on how to access variables and other Chado content within the template files.</p></li>
-     </li>
-
-     <li><p><b>Adding Links to the "Resources" Sidebar</b>: If you use the pre-set default Tripal layout for theming, you
-     will see a "Resources" sidebar on each page.  The links that appear on the sidebar are automatically generated
-     using Javascript for all of the stock "Blocks" that appear on the page. If you want to add additional links
-     (e.g. a dynamic link to additional stock content) and you want that link to appear in the
-     "Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the
-     section at the bottom of the template file where the resources section is found.</p></li>
-
-     </ul>
-   </p>