Welcome to Tripal’s documentation!

Contents:

• Tripal v3 User’s Guide
  • What Is Tripal?
  • Install Tripal
    • Pre-planning
      • IT Infrastructure
      • Technical Skills
      • Development and Production Instances
    • DRUPAL_HOME Variable
    • Server Setup
      • Server Setup (Ubuntu 18.04 LTS)
      • Server Setup (Ubuntu 16.04 LTS)
      • Server Setup (CentOS 7)
    • Drush Installation
      • Install Drush
    • Installation Method #1: Rapid Installation
      • Database Setup
      • Tripal Installation
    • Installation Method #2: Step-by-Step Manual Installation
      • Drupal Installation
      • Tripal Prerequisites
      • Tripal Installation
    • Upgrade from Tripal v2 to v3
      • Step 1: Upgrade Tripal
      • Step 2: Migrate Content
      • Step 3: Use Legacy Templates (optional)
      • Step 4: Delete Tripal v2 Content and Publish Tripal v3 Content
      • Troubleshooting
    • Automating Job Execution
      • Automating Tripal Tasks
    • Theming your Site
      • Changing the Look-and-Feel
      • Customizing a Theme
  • Brief Drupal Overview
    • User Account Page
    • Creating Content
    • Finding Content
    • Site Administration
      • Modules
      • Themes
      • Blocks
      • Menus
      • URL Path
      • Site Configuration
    • User Accounts
  • Learn Chado
  • Working with Content Types
    • Creating Content Types
      • Find a Controlled Vocabulary (CV) Term
      • How to Add a CV Term
      • Create a Tripal Content Type
    • Setting Page Titles and URLs
      • Setting Page Titles
      • Setting URLs
    • Configuring Page Layout
      • Rearranging Fields
      • Removing Fields and/or Field Labels
      • Changing Tripal Pane Names
      • Display/Hide Tripal Panes on Page Load
    • Hide Empty Fields and AJAX loading
      • Hiding Empty Fields
      • Using AJAX to Load Fields
    • Field Specific Permissions
      • Why Field Permissions?
      • Installing the Drupal Field Permissions module
      • Setting Field-specific Permissions
    • Handling Orphaned Entities
  • Setup of an Example Site
    • Organisms
      • Creating an Organism Page
      • Load data from NCBI Taxonomy
      • Adding New Fields
      • Further Customizations
    • Analyses
    • Cross References
    • Controlled Vocabularies
    • Genomes and Genes
      • Loading Feature Data
      • Loading a GFF3 File
      • Loading FASTA files
      • Creating Gene Pages
      • Customizing Transcripts on Gene Pages
    • Importing Publications
      • Manually Adding a Publication
      • Import of Publications
      • Import from the USDA National Agricultural Library
    • Functional Annotations
      • Module Setup
      • Adding BLAST Results
      • Adding InterProScan Results
      • Adding KEGG Results
      • Managing Gene Ontology Annotations
  • File Management
    • User Quotas
    • User’s Files
  • Materialized Views
  • Custom Tables
  • Searching
    • Tripal Content-Specific Search Tools
    • Search API Module: Site-Wide Searching
      • Installing Drupal Search API
      • Define your Search Backend/Server
      • Define a Search Index
      • Creating a Search Interface for your users
      • Configuring What is displayed for each Search Result
      • Adding the Keywords Search Box
      • Sort by “Relevance”
      • Only Show results when user clicks Search
    • Tripal Elasticsearch Module
  • Job Management (Tripal Daemon)
    • Features
    • Installation
    • Usage
  • Web Services
    • Overview
    • Enable Web Services
    • Exploring Web Services
    • Structure of a Web Service Response
    • Primary Services
    • The Content Service
    • Content Type Listing
    • Content Type Members (Entities)
    • Content (Entity) Resource
    • Searching for Content
    • Searching Limitations
    • Hiding or Adding Content
  • Bulk Loader
    • Plan How to Store Data
    • Creating a New Bulk Loader Template
    • Creating a Bulk Loader Job (importing a file)
    • Sharing Your Templates with Others
  • Customizing Your Site
• Developer’s Guide
  • Introduction to the Tripal API
    • Requirements
  • Tripal Data Structures
    • Bundles (Content Types)
    • Entity
    • Fields
    • Field Instances
    • Entity Types
  • Module Development Best Practice
    • The Drupal Devel Module
    • Add your module to Tripal.info
    • Coding Best Practices
      • Host your code on GitHub
      • Associate the GitHub repository with Tripal
      • DOIs
      • Testing and Continuous Integration
      • Documentation
      • Coding Standards
  • Accessing Chado
    • The Chado Query API
      • Generic Queries to a specific chado table
      • Generic Queries for any SQL
      • Loading of Variables from chado data
    • The Chado Schema API
      • Ensuring columns Tables & Columns exist
      • Checking the Schema Version
      • Retrieving a list of tables
      • Ensuring your Chado instance is compliant
      • Schema Definition
  • Creating Custom Modules
  • Creating a Custom Field
    • Selecting Vocabulary Terms
      • Ontologies: what and why?
      • Storage of Terms in Chado
      • Vocabulary Short Names and Namespaces
    • Manual Field Creation
      • Directory Structure for Fields
      • Anatomy of the ChadoField Class
      • Static Member Variables
      • The load() function.
      • elementInfo() function
      • query() function
    • Creating a Custom Widget
      • The Form
      • Validation
      • Saving the Data
    • Creating a Custom Formatter
      • The view() function.
      • Creating Pagers
      • The settingsForm() Function.
      • The settingsSummary() Function.
    • AJAX Responsive Formatters
      • Drupal and AJAX
      • Example form and field
    • Attach Fields to Content Types
      • The hook_bundle_fields_info() function
      • Programmatically Attaching Fields
      • Allowing Manual Attachment of Fields
    • Easier Field Creation: Tripal Field Generator
  • Exporting Field Settings With Drupal Features
    • Why Drupal Features?
      • Version control
      • How many Features?
      • A Hazard: Mapping bundle IDs
    • Drupal Features Tutorial
      • Configuring the bundle fields
      • Exporting the bundle field displays
      • Importing the feature configuration
  • Creating Custom Data Loaders
    • Create a Custom Module
    • Create the Class File
    • Static Variables
    • Form Components
      • The form function
      • The formValidate function
    • Importer Execution
      • The run function
      • Importing the File
    • Logging and Progress
      • The logMessage function
      • The setTotalItems and setItemsHandled functions
    • Testing Importers
      • Example file
      • Loading the Importer
  • Creating Custom Web Services
    • Introduction
    • Getting Started
    • Documenting the Services
    • Implementing a Collection Resource
    • Simplifying the Property Keys
    • Implementing a Resource
    • Documenting Properties
    • More on Parameters
    • Implementing Other Operations
    • Controlling Access to Resources
  • Continuous Integration
    • Using GitHub Workflows
      • Telling GitHub about your workflow
      • Configuring a workflow to run PHPUnit tests
    • Checking your Action
    • Adding the Badge to your README
  • Using ReadTheDocs
    • What is ReadTheDocs?
    • How do I add ReadTheDocs to my project?
    • What should my documentation include?
  • Video Tutorials
    • Testing
    • Developer Tools
    • Other
• Extension Modules
  • Administrative
    • Private BioData
    • Tripal Alchemist
    • Tripal Curator
    • Tripal HeadQuarters
  • Analysis/Annotation
    • Tripal Analysis Expression
    • Tripal Analysis Blast
    • Tripal Analysis KEGG
    • Tripal Analysis Interpro
    • Tripal CV-Xray
    • Tripal OrthoQuery
  • Breeding
    • BIMS
  • Data Loading/Collection
    • Genotype Loader
    • Mainlab Chado Loader
    • Raw Phenotypes
    • Tripal BibTeX
    • Tripal Plant PopGen Submission
    • Migrate Chado
  • Developer Tools
    • TripalDock
    • Tripal Download API
    • Tripal D3.js API
    • Tripal Fields Generator
    • Tripal Rapid Installer
    • Tripal Test Suite
  • Third-party Integration
    • BrAPI
    • Tripal Blast
    • Tripal Galaxy
    • Tripal JBrowse
    • VCF Filter
  • Searching
    • CartograTree
    • Mainlab Chado Search
    • Tripal ElasticSearch
    • Tripal MegaSearch
    • Tripal Sequence Similarity Search
  • Visualization/Display
    • Analyzed Phenotypes
    • CvitEmbed
    • Mainlab Tripal Data Display
    • ND Genotypes
    • Phylotree
    • Tripal Fancy Fields
    • Tripal MapViewer
  • In Development
    • Tripal Apollo
    • Tripal Multi-Chado
  • Tripal Module Rating System
    • Bronze
    • Silver
    • Gold
    • Rate your Extension Module!
  • Adding your Module to this list!
    • Instructions
    • Guidelines
• Tripal Community
  • Guidelines for Contribution to Tripal
    • Github Communication Tips
    • Bugs
    • Feature Requests
    • Pull Request (PR) Guideline
      • How to create a PR
    • How PRs and Issues are Handled
    • Code of Conduct
    • Testing/CI
  • Unit Tests for Tripal
    • Tripal Test Suite
      • Installation
    • Testing criteria
    • Test organization
      • Submodules
      • Categories
    • Writing tests
      • Tagging tests
      • Defining the test class
      • Defining individual tests
      • Testing quietly
  • Contributing to the Documentation
    • Guide
      • Install Sphinx
      • Building your changes
      • Tripal conventions
  • Tripal Governance
    • Adopters
    • Extension Contributors
    • Core Code Contributors
    • Committers
    • The Tripal Project Management Committee (PMC)
      • Communication and Meetings
    • Tripal Advisory Committee (TAC)
      • Membership
      • TAC Chair
      • TAC Meeting Agenda Items
      • Communication and Meetings
    • Changes to this Document
  • Funding Proposal Development