Extension module docs: Added more modules from tripal.info.

docs/extensions.rst

@@ -7,14 +7,22 @@ The below modules are Tripal 3 compatible and grouped roughly by category:
    :maxdepth: 2
 
    extensions/administrative
-   extensions/annotation
+   extensions/analysis
+   extensions/datainput
    extensions/developer
    extensions/3rdparty
+   extensions/search
    extensions/visualization
 
+If you don't see the module you are looking for here, try a `Tripal-specific search on GitHub <https://github.com/search?q=topic%3Atripal>`__.
+
+Add your Module to this list!
+-----------------------------
+
 **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.
 
-**Instructions:**
+Instructions
+^^^^^^^^^^^^^
 
 1. From the current page, click the category in the list above that best fits your module.
 2. Click the "Edit on Github" link at the top of the page.
@@ -30,9 +38,11 @@ The below modules are Tripal 3 compatible and grouped roughly by category:
   `Documentation <https://yourmodule.readthedocs.io/en/latest/index.html>`__
   `Repository <https://github.com/you/yourmodule>`__
 
-**Guidelines:**
+Guidelines
+^^^^^^^^^^^
 
 - Make sure to follow alphabetical order when choosing where on the category page to add your module.
 - Please write two sentences MAXIMUM about the function of the module.
 - Include links to both the documentation (even if it's your README) and the repository (e.g. Github, Gitlab)
 - If your module doesn't fit well in any of the existing categories, still pick the best one but then feel free to suggest a new category in the PR description.
+- Extension Modules must be publically available for download

docs/extensions/3rdparty.rst

@@ -11,14 +11,6 @@ This module provides a basic interface to allow your users to utilize your serve
 `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
 -------------
 

docs/extensions/datainput.rst

@@ -0,0 +1,20 @@
+Data Loading/Collection
+=======================
+
+The following modules provide interfaces for collection and/or loading of biological data.
+
+Mainlab Chado Loader
+---------------------
+
+MCL (Mainlab Chado Loader) is a module that enables users to upload their biological data to chado database schema. Users are required to transfer their biological data into various types of data template files. MCL, then, uploads these data template files into a chado schema.
+
+`Documentation <https://gitlab.com/mainlabwsu/mcl/blob/master/README.md>`__
+`Repository <https://gitlab.com/mainlabwsu/mcl>`__
+
+Tripal Plant PopGen Submission
+-------------------------------
+
+The Tripal Plant PopGen Submit (TPPS) Module supports a flexible submission interface for genotype, phenotype, environmental, and metadata for population, association, or landscape genetics studies. The portal walks the user through specific questions and collects georeferenced coordinates on plant accessions and also supports ontology standards, including the Minimal Information About a Plant Phenotyping Experiment (MIAPPE) (http://www.miappe.org/) and standard genotyping file formats, such as VCF.
+
+`Documentation <https://tpps.readthedocs.io/en/latest/>`__
+`Repository <https://gitlab.com/TreeGenes/TGDR>`__

docs/extensions/search.rst

@@ -0,0 +1,34 @@
+Searching
+==========
+
+CartograTree
+-------------
+
+CartograTree is a web-based application that allows researchers to identify, filter, compare, and visualize geo-referenced biotic and abiotic data. Its goal is to support numerous multi-disciplinary research endeavors including: phylogenetics, population structure, and association studies.
+
+`Documentation <https://gitlab.com/TreeGenes/CartograTree/blob/master/README.md>`__
+`Repository <https://gitlab.com/TreeGenes/CartograTree>`__
+
+Mainlab Chado Search
+---------------------
+
+Mainlab Chado Search is a module that enables advanced search function for biological data stored in a Tripal/Chado database. By default, a set of search interfaces are provided, such as 'Gene Search' for searching genes and/or transcripts, 'Marker Search' for searching genetic markers, and 'Sequence Search' for searching any sequences stored in the Chado feature table. Searches for other data types, such as QTL, Map, Trait, Stock, Organism are also provided but may require modification to the materialized view to adjust for site-specific data storage.
+
+`Documentation <https://gitlab.com/mainlabwsu/chado_search/blob/master/README.md>`__
+`Repository <https://gitlab.com/mainlabwsu/chado_search>`__
+
+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 Sequence Similarity Search
+----------------------------------
+
+This module supports sequence similarity search on a Tripal website through a new dual application option. The Tripal module provides access to the speed increase available through Diamond for BLASTP/BLASTX style searches as well as traditional NCBI BLAST for BLASTN. Both applications are integrated into a single interface that provides file upload or copy/paste sequence support for the query and access to formatted databases for NCBI BLAST or Diamond. The target databases can be customized for the categories of whole genome, gene, protein, and transcriptome/unigene. The administration interface allows the admin user to set what pre-indexed databases are available (which show up in a dropdown menu). The module supports execution of the searches on a remote machine so that the search is not running directly on the limited resources typically associated with web servers.
+
+`Documentation <https://github.com/Ferrisx4/tripal_diamond/blob/master/README.md>`__
+`Repository <https://github.com/Ferrisx4/tripal_diamond>`__

docs/extensions/visualization.rst

@@ -1,8 +1,16 @@
-Visualization
-==============
+Visualization/Display
+======================
 
 The following modules provide specialized displays for Tripal content types.
 
+Mainlab Tripal Data Display
+----------------------------
+
+Mainlab Tripal Data Display contains a set of Drupal/PHP templates that organize and extend the default display of the biological data hosted on a Tripal-enabled site (i.e. http://tripal.info). Supported data type includes orgainsm, marker, QTL, germplasm (stock), map (featuremap), project, heritable phenotypic marker (MTL), environment (ND geolocation), haplotype block, polymorphism, eimage, generic gene (genes created by parsing Genbank files using the Mainlab 'tripal_genbank_parser' module), feature, and pub. Each of the templates can be turned on/off as desired.
+
+`Documentation <https://gitlab.com/mainlabwsu/mainlab_tripal/blob/master/README.md>`__
+`Repository <https://gitlab.com/mainlabwsu/mainlab_tripal>`__
+
 Tripal Fancy Fields
 -------------------
 
@@ -10,3 +18,11 @@ This module provides additional fields for use with Tripal 3. The current versio
 
 `Documentation <https://github.com/tripal/trpfancy_fields/blob/master/README.md>`__
 `Repository <https://github.com/tripal/trpfancy_fields>`__
+
+TripalMap
+----------
+
+TripalMap MapViewer module displays map data stored in Chado. MapViewer provides interfaces to view all linkage groups of a map, choose a linkage group and zoom in to a specific region of a linkage group, compare maps that share the same markers and change colors of markers/QTL. The interface can be integrated into Tripal map page and hyperlinked to/from any Tripal page that are displayed in maps (marker, QTL, heritable morphological marker and/or gene). The admin page allows site developers some flexibility in the display pattern. Allows Tripal based databases to provide users functionality similar to GMOD-CMap without having to maintain a separate underlying database. The map display is built from the data in Materialized Views for both better performance and flexibility of the way the data is stored in
+
+`Documentation <https://gitlab.com/mainlabwsu/tripal_map/blob/master/README.md>`__
+`Repository <https://gitlab.com/mainlabwsu/tripal_map>`__