Merge pull request #754 from tripal/402_rtd_module_list

Extension Module list on ReadtheDocs

docs/_static/theme_overrides.css

@@ -12,11 +12,51 @@ See: https://rackerlabs.github.io/docs-rackspace/tools/rtd-tables.html
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+}
 
-/** 
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docs/extensions.rst

@@ -0,0 +1,49 @@
+Extension Modules
+==================
+
+The below modules are Tripal 3 compatible and grouped roughly by category:
+
+.. toctree::
+   :maxdepth: 2
+
+   extensions/administrative
+   extensions/analysis
+   extensions/data_input
+   extensions/developer
+   extensions/3rd_party
+   extensions/search
+   extensions/visualization
+   extensions/in_development
+
+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
+^^^^^^^^^^^^^
+
+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.
+3. Add your module using the following template.
+
+.. code:: RST
+
+  Module Name
+  ------------
+
+  This module loads in X, Y, and Z.  It provides admin for A and B, and user area C.
+
+  `Documentation <https://yourmodule.readthedocs.io/en/latest/index.html>`__
+  `Repository <https://github.com/you/yourmodule>`__
+
+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 publicly available for download

docs/extensions/3rd_party.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 Galaxy
+-------------
+
+This module is for integration of Tripal and the Galaxy Project. It facilitates 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>`__
+
+VCF Filter
+-----------
+
+This modules provides a form interface so users can custom filter existing VCF files and export in a variety of formats. The form simply provides an interface to VCFtools and uses the Tripal Download API to provide the filtered file to the user.
+
+`Documentation <https://github.com/UofS-Pulse-Binfo/vcf_filter/blob/master/README.md>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/vcf_filter>`__

docs/extensions/administrative.rst

@@ -0,0 +1,29 @@
+Administrative
+==============
+
+The following modules provide support to Tripal site administrators.
+
+Tripal Alchemist
+-----------------
+
+Tripal Alchemist allows you to transform entities from one type to another.  Define multiple bundles with the same base table and easily convert existing entities to the new type.
+
+`Documentation <https://github.com/statonlab/tripal_alchemist/blob/master/README.md>`__
+`Repository <https://github.com/statonlab/tripal_alchemist>`__
+
+
+Tripal Curator
+-------------------------
+
+Tripal Curator is a Toolbox for curating Chado Properties.  Split properties into multiple child properties, and mass reassign property CVterms.
+
+`Documentation <https://github.com/statonlab/tripal_curator/blob/master/README.md>`__
+`Repository <https://github.com/statonlab/tripal_curator>`__
+
+Tripal HeadQuarters
+-------------------
+
+Tripal HeadQuarters (HQ) provides an administrative layer for Tripal, giving users limited access to content creation forms which must be approved by an admin before they are inserted into the database. Admins can use Chado-specific permissions to define organism or project-specific administrative rights.
+
+`Documentation <https://tripal-hq.readthedocs.io/en/latest/index.html>`__
+`Repository <https://github.com/statonlab/tripal_hq>`__

docs/extensions/analysis.rst

@@ -0,0 +1,43 @@
+Analysis/Annotation
+===================
+
+The following modules provide support for loading annotation or analysis' into Chado and displaying them on Tripal pages.
+
+Tripal Analysis Expression
+--------------------------
+
+A module for loading, annotating, and visualizing NCBI Biomaterials and expression data.
+
+`Documentation <https://github.com/tripal/tripal_analysis_expression/blob/master/README.md>`__
+`Repository <https://github.com/tripal/tripal_analysis_expression>`__
+
+Tripal Analysis Blast
+---------------------
+
+This module extends the Tripal Analysis Module and provides a method for loading XML results from the NCBI blast program. Blast results appear on each feature page.
+
+`Documentation <https://tripal.readthedocs.io/en/latest/user_guide/example_genomics/func_annots/blast.html>`__
+`Repository <https://github.com/tripal/tripal_analysis_blast>`__
+
+Tripal Analysis KEGG
+--------------------
+
+This module provides a method for loading of KEGG ortholog assignments derived from the KEGG Automated Annotation Server (KAAS). KEGG assignments appear on each feature page, and a full KEGG report is available for browsing results once uploaded.
+
+`Repository <https://github.com/tripal/tripal_analysis_kegg>`__
+
+Tripal Analysis Interpro
+------------------------
+
+This module provides a method for loading XML results from the InterProScan program. The module can load InterProScan XML v4 or InterProScan XML v5 generated from the command-line or web-based versions of InterProScan. Additionally, GO terms mapped by InterProScan can optionally be assigned to features.
+
+`Documentation <https://tripal.readthedocs.io/en/latest/user_guide/example_genomics/func_annots/interpro.html>`__
+`Repository <https://github.com/tripal/tripal_analysis_interpro>`__
+
+Tripal CV-Xray
+--------------
+
+Tripal CV-Xray maps content annotations onto controlled vocabulary trees.  The end result is a browseable CV field that lets users explore ontologies and find associated content.
+
+`Documentation <https://github.com/statonlab/tripal_cv_xray/blob/master/README.md>`__
+`Repository <https://github.com/statonlab/tripal_cv_xray>`__

docs/extensions/data_input.rst

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+Data Loading/Collection
+=======================
+
+The following modules provide interfaces for collection and/or loading of biological data.
+
+Genotype Loader
+----------------
+
+A Drush-based loader for VCF files that follows the genotype storage rules outline by ND genotypes. It has been optimized to handle very large files and supports customization of ontology terms used.
+
+`Documentation <https://genotypes-loader.readthedocs.io/en/latest/>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/genotypes_loader>`__
+
+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>`__
+
+Raw Phenotypes
+---------------
+
+This module was designed to aid in collection and further analysis of raw phenotypic data. It supports Excel drag-n-drop uploads with immediate validation and researcher feedback. Additionally, it provides summary charts and download functionality.
+
+`Documentation <https://github.com/UofS-Pulse-Binfo/rawphenotypes/blob/master/README.md>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/rawphenotypes>`__
+
+Tripal BibTeX
+--------------
+
+A BibTEX importer for Tripal Publications. Currently this module only provides a Drush function (``tripal-import-bibtex-pubs``; ``trpimport-bibtex``) for import of BibTEX files.
+
+`Documentation <https://github.com/UofS-Pulse-Binfo/tripal_bibtex/blob/7.x-3.x/README.md>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/tripal_bibtex>`__
+
+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/developer.rst

@@ -0,0 +1,53 @@
+
+Developer Tools
+===============
+
+The following modules provide support to both core and extension Tripal developers.
+
+TripalDock
+------------
+
+TripalDock is a command line tool that helps with creating and running Tripal sites using Docker. This tool is designed for developers and is not suitable for production.
+
+`Documentation <https://github.com/statonlab/tripaldock/blob/master/README.md>`__
+`Repository <https://github.com/statonlab/tripaldock>`__
+
+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
+-----------------------
+
+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
+-----------------
+
+Tripal Test Suite is a composer package that handles common test practices such as bootstrapping Drupal before running the tests, creating test file, creating and managing database seeders (files that seed the database with data for use in testing) and much more.
+
+`Documentation <https://tripaltestsuite.readthedocs.io/en/latest/>`__
+`Repository <https://github.com/tripal/TripalTestSuite>`__

docs/extensions/in_development.rst

@@ -0,0 +1,22 @@
+
+In Development
+==============
+
+The following modules are not yet ready for production or not fully Tripal 3 compatible.
+
+
+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.
+
+`Documentation <https://gitlab.com/mainlabwsu/tripal_map/blob/master/README.md>`__
+`Repository <https://gitlab.com/mainlabwsu/tripal_map>`__
+
+Tripal Apollo
+--------------
+
+Tripal Apollo lets you manage user accounts for your JBrowse Apollo instances on your Tripal site.  Provides a form to request apollo access, an Apollo instance content type that connects to Chado Organisms, and an administrative interface for managing requests.
+
+`Documentation <https://tripal-apollo.readthedocs.io/en/latest/>`__
+`Repository <https://github.com/NAL-i5K/tripal_apollo>`__

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

@@ -0,0 +1,44 @@
+Visualization/Display
+======================
+
+The following modules provide specialized displays for Tripal content types.
+
+Analyzed Phenotypes
+--------------------
+
+This module provides support and visualization for partially analyzed data stored in a modified GMOD Chado schema. It is meant to support large scale phenotypic data through backwards compatible improvements to the Chado schema including the addition of a project and stock foreign key to the existing phenotype table, optimized queries and well-chosen indexes.
+
+`Documentation <https://analyzedphenotypes.readthedocs.io/en/latest/index.html>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/analyzedphenotypes>`__
+
+CvitEmbed
+----------
+
+This module integrates `CViTjs <https://github.com/LegumeFederation/cvitjs>`__ with Tripal to provide whole-genome visualizations. It creates one page per plot and makes them accessible via the Drupal Navigation menu.
+
+`Documentation <https://github.com/UofS-Pulse-Binfo/cvitembed/blob/master/README.md>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/cvitembed>`__
+
+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 organism, 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>`__
+
+ND Genotypes
+-------------
+
+This module provides support and visualization of genotypic data stored in a modified GMOD Chado schema. The 3.x branch of this module represents a shift towards support for large scale genotypic datasets through backwards compatible improvements to the Chado schema including a new gathering table for genotypes (genotype_call) modeled after the Chado phenotype table, optimized queries and well-chosen indexes.
+
+`Documentation <https://nd-genotypes.readthedocs.io/en/latest/>`__
+`Repository <https://github.com/UofS-Pulse-Binfo/nd_genotypes>`__
+
+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>`__

docs/index.rst

@@ -12,3 +12,4 @@ Welcome to Tripal's documentation!
 
    user_guide
    dev_guide
+   extensions