Tripal is a toolkit for construction of online biological (genetics, genomics,
breeding, etc), community database, and is a member of the
[GMOD](http://www.gmod.org) family of tools. Tripal v3 provides by default
integration with the [GMOD Chado database](http://gmod.org/wiki/Chado_-_Getting_Started).
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](http://drupal.org/project/views)
* [Entity API](http://drupal.org/project/entity)
* 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 '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.