tripal

Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database, and is a member of the GMOD family of tools. Tripal v3 provides by default integration with the GMOD Chado database. Tripal's primary goals are:

Genomics, genetics, breeding and other biological data are increasingly complicated and time consuming to publish online for other researchers to search, browse and make discoveries. Tripal provides a framework to reduce the complexity of creating such a site, and provides access to a community of similar groups that share community-standards, and interact to address questions and learn best practices for sharing, storing and visualizing complex biological data.

1. Provide a framework for those with genomic, genetic and breeding data that can facility creation of an online site for display, search and visualization.
2. To use community-derived standards and ontologies to facility continuity between sites which in turn fosters collaboration and sharing
3. Provide an out-of-the-box setup for a genomics site for those who simply want to put new genome assemblies and annotations online.
4. Provide Application Programming Interfaces (APIs) for complete customization such that more advanced displays, look-and-feel, and new functionality can be supported.

Features

The following major features are available in Tripal v3.

• Tripal v3's design is centered around controlled vocabularies and ontologies. This allows for greater integration with the semantic web and will help support data exchange between Tripal sites.
• RESTful web services. Tripal v3 introduces RESTful web services for Tripal. The resources provided by these web services uses JSON-LD and WC3 Hydra vocabulary to deliver content.
• Tripal v3 introduces new content pages. In older versions of Tripal all content was provided via Drupal "nodes". Now content is delivered using new content types (e.g. gene, genetic_marker, organism, germplasm, etc.) and the site admin controls which content types are available on the site.
• Chado support:
  • Tripal v3 represents a major redesign from previous versions. Previously, Chado was the only storage backend supported. Tripal v3 provides by default support for Chado, but also sports a new design that affords integration of other storage backends (including noSQL options).
    
  • A Chado v1.2 or v1.3 installer
  • Data loaders for ontologies (controlled vocabularies), GFF files, and FASTA files, publications (from PubMed and AGIRCOLA).
  • Generic Bulk Data Loader Modules allows for creation of custom loaders without programming (requires an understanding of Chado).
  • Supports creation of materialized views for faster data queries.

Required Dependencies

• Drupal:
  • Drupal 7.x
  • Drupal core modules: Search, Path and PHP modules.
  • Drupal contributed modules:
  • Views
  • Entity API
• PostgreSQL
• PHP 5.5+
• UNIX/Linux

Installation

Please follow the instructions in the online Tripal User's Guide: http://tripal.info/tutorials/v2.0/installation

Upgrade from Tripal v2.x to v3.x

Note: Upgrade can only be performed using the drush command.

Note: Deprecated API functions from Tripal v1.x have been removed from Tripal v3. Therefore, use of deprecated API functions in templates or custom modules may cause a white screen of death (WSOD). Check teh server logs if this occurs to find where deprecated functions may be used.

Upgrade Instructions:

Step 1: Put the site in maintenance mode.

Step 2: Disable tripal modules. Disabling the core module will disable all other Tripal modules:

drush pm-disable tripal_core

Step 3: Remove old Tripal v2 package and replace with Tripal v3 package Step 4: Enable the tripal module

drush pm-enable tripal

Step 5: Enable the tripal_chado module

drush pm-enable tripal_chado

Step 6: Tripal v2 modules are now called 'legacy modules'. these are the modules that were disabled in step #2. For backwards compatibility, you should re-enable these modules:

  drush pm-enable tripal_core, tripal_views, tripal_db, tripal_cv, \
    tripal_analysis, tripal_organism, tripal_feature, tripal_pub, \
    tripal_stock

Be sure to enable any additional modules not included in the example drush command above.

Step 7: Return to your Tripal site, and click the link that appears for preparing Chado and launch the job.

Customization

Tripal can be used “as is” but also allows for complete customization. PHP-based template files are provided for all data types to allow for precise customizations as required by the community. A well-developed Tripal API provides a uniform set of variables and functions for accessing any and all data within the Chado database. See the Tripal 3.x Developer's Handbook for additional details.

Development Testing

To run PHP unit tests on your local system, run composer install to install developer-specific requirements. Next, create a .env file in your /Tests/ directory that defines the DRUPAL_ROOT variable, for example

DRUPAL_ROOT=/var/www/html

Then run PHPUnit from your root Tripal directory.

PHPUnit tests will also be run in the Travis CI build.