Extension module docs: Added more modules from github.

docs/extensions.rst

@@ -1,15 +1,16 @@
 Extension Modules
 ==================
 
-The below modules are Tripal 3 compatible and grouped roughly by category.
+The below modules are Tripal 3 compatible and grouped roughly by category:
 
 .. toctree::
    :maxdepth: 2
-   :caption: Categories
 
    extensions/administrative
    extensions/annotation
    extensions/developer
+   extensions/3rdparty
+   extensions/visualization
 
 **We would love for you to contribute your own module to this list!** This is done by creating a Pull Request (PR) to `Tripal <https://github.com/tripal/tripal>`__ modify our documentation.
 

docs/extensions/3rdparty.rst

@@ -0,0 +1,36 @@
+Third-party Integration
+=======================
+
+The following modules provide integration with external third-party tools. For example, they may allow you to easily embed the tool in Drupal/Tripal pages and/or expose data from the tool on your Tripal site.
+
+Tripal Blast
+------------
+
+This module provides a basic interface to allow your users to utilize your server's NCBI BLAST+. There is a simple interface allowing users to paste or upload a query sequence and then select from available databases and a tabular results listing with alignment information and multiple download formats (HTML, TSV, GFF3, XML) available.
+
+`Documentation <https://github.com/tripal/tripal_blast/blob/7.x-1.x/README.md>`__
+`Repository <https://github.com/tripal/tripal_blast>`__
+
+Tripal ElasticSearch
+--------------------
+
+The Tripal Elasticsearch module allows you to easily manage the indexing and display of Elasticsearch on your Tripal website. It also easily enables Cross-Site Querying, allowing you to connect to other Tripal sites and provide additional search results to your users.
+
+`Documentation <https://github.com/tripal/tripal_elasticsearch/blob/master/docs/README.md>`__
+`Repository <https://github.com/tripal/tripal_elasticsearch>`__
+
+Tripal Galaxy
+-------------
+
+This module is for integration of Tripal and the Galaxy Project. It facillitates the creation of forms on your Tripal site that submit jobs to a galaxy instance.
+
+`Documentation <https://github.com/tripal/tripal_galaxy/blob/7.x-1.x/README.md>`__
+`Repository <https://github.com/tripal/tripal_galaxy>`__
+
+Tripal JBrowse
+--------------
+
+This module provides integration between Tripal sites and pre-existing GMOD JBrowse instances. It allows you to create pages on your Tripal site with an embedded JBrowse instance by filling out a simple form.
+
+`Documentation <https://github.com/tripal/tripal_jbrowse/blob/7.x-2.1.x/README.md>`__
+`Repository <https://github.com/tripal/tripal_jbrowse>`__

docs/extensions/administrative.rst

@@ -1,6 +1,8 @@
 Administrative
 ==============
 
+The following modules provide support to Tripal site administrators.
+
 Tripal Alchemist
 -----------------
 
@@ -18,16 +20,6 @@ Tripal Property Curations is a Toolbox for curating Chado Properties. It is unde
 `Documentation <https://github.com/statonlab/tripal_curator/blob/master/README.md>`__
 `Repository <https://github.com/statonlab/tripal_curator>`__
 
-
-Tripal ElasticSearch
---------------------
-
-The Tripal Elasticsearch module allows you to easily manage the indexing and display of Elasticsearch on your Tripal website. It also easily enables Cross-Site Querying, allowing you to connect to other Tripal sites and provide additional search results to your users.
-
-`Documentation <https://github.com/tripal/tripal_elasticsearch/blob/master/docs/README.md>`__
-`Repository <https://github.com/tripal/tripal_elasticsearch>`__
-
-
 Tripal HeadQuarters
 -------------------
 

docs/extensions/annotation.rst

@@ -1,6 +1,8 @@
 Analysis/Annotation
 ===================
 
+The following modules provide support for loading annotation or analysis' into Chado and displaying them on Tripal pages.
+
 Tripal Analysis Expression
 --------------------------
 
@@ -32,14 +34,6 @@ This module provides a method for loading XML results from the InterProScan prog
 `Documentation <https://tripal.readthedocs.io/en/latest/user_guide/example_genomics/func_annots/interpro.html>`__
 `Repository <https://github.com/tripal/tripal_analysis_interpro>`__
 
-Tripal JBrowse
---------------
-
-This module provides integration between Tripal sites and pre-existing GMOD JBrowse instances. It allows you to create pages on your Tripal site with an embedded JBrowse instance by filling out a simple form.
-
-`Documentation <https://github.com/tripal/tripal_jbrowse/blob/7.x-2.1.x/README.md>`__
-`Repository <https://github.com/tripal/tripal_jbrowse>`__
-
 Tripal CV-Xray
 --------------
 
@@ -47,11 +41,3 @@ Tripal CV-Xray maps content annotations onto controlled vocabulary trees.  The e
 
 `Documentation <https://github.com/statonlab/tripal_cv_xray/blob/master/README.md>`__
 `Repository <https://github.com/statonlab/tripal_cv_xray>`__
-
-Tripal Galaxy
--------------
-
-This module is for integration of Tripal and the Galaxy Project. It facillitates the creation of forms on your Tripal site that submit jobs to a galaxy instance.
-
-`Documentation <https://github.com/tripal/tripal_galaxy/blob/7.x-1.x/README.md>`__
-`Repository <https://github.com/tripal/tripal_galaxy>`__

docs/extensions/developer.rst

@@ -2,6 +2,32 @@
 Developer Tools
 ===============
 
+The following modules provide support to both core and extension Tripal developers.
+
+Tripal Docker (Centos)
+----------------------
+
+This repository builds docker images for Tripal v2 and Tripal v3 installed upon Drupal 7.56 with PostGreSQL database.
+
+`Documentation <https://github.com/tripal/docker-tripal-centos/blob/master/README.md>`__
+`Repository <https://github.com/tripal/docker-tripal-centos>`__
+
+Tripal Download API
+--------------------
+
+This module provides an API for downloading Tripal/Chado data. Since download functionality is often sought after for Tripal sites and Views Data Export is not currently meeting our needs, this module aims to provide an API to aid module and site developers in making efficient, user friendly downloads available.
+
+`Documentation <https://github.com/tripal/trpdownload_api/blob/7.x-1.x/README.md>`__
+`Repository <https://github.com/tripal/trpdownload_api>`__
+
+Tripal D3.js API
+-----------------
+
+Provides d3.js integration for Tripal. It provides an API for developing consistent biological diagrams with a common configuration, as well as, providing some common diagrams such as pie, bar, column and pedigree diagrams.
+
+`Documentation <https://github.com/tripal/tripald3/blob/7.x-1.x/README.md>`__
+`Repository <https://github.com/tripal/tripald3>`__
+
 Tripal Fields Generator
 -----------------------
 
@@ -10,6 +36,14 @@ This is a CLI tool to help automate the generation of Tripal fields.
 `Documentation <https://github.com/tripal/fields_generator/blob/master/README.md>`__
 `Repository <https://github.com/tripal/fields_generator>`__
 
+Tripal Rapid Installer
+----------------------
+
+Provides rapid installation of a Tripal site using Drush.
+
+`Documentation <https://github.com/tripal/tripal_install/blob/master/README.md>`__
+`Repository <https://github.com/tripal/tripal_install>`__
+
 Tripal Test Suite
 -----------------
 

docs/extensions/visualization.rst

@@ -0,0 +1,12 @@
+Visualization
+==============
+
+The following modules provide specialized displays for Tripal content types.
+
+Tripal Fancy Fields
+-------------------
+
+This module provides additional fields for use with Tripal 3. The current version provides a single-series chart field that can be displayed as a pie, donut, or bar chart, as well as, a simple table.
+
+`Documentation <https://github.com/tripal/trpfancy_fields/blob/master/README.md>`__
+`Repository <https://github.com/tripal/trpfancy_fields>`__