tripal/README.txt

What is Tripal?
--------------
Tripal is a collection of open-source freely available Drupal modules 
and is a member of the GMOD family of tools. Tripal serves as a web 
interface for the GMOD Chado database and is designed to reduce the
time and cost required for construction of an online genomic, genetic
and breeding database.


Features
--------------
 - a Chado 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 
   loading templates.
 - Drupal nodes (web pages) are automatically generated for organisms,
   genomic features, biological libraries, and stocks
 - Supports creation of materialized views for faster data queries.
 - Display templates are provided for all content types for
   easier customization.
 - Views Integration allows for custom listings of data
 - Content pieces exposed as blocks allowing the use of Panels for 
   custom layouts of Tripal Nodes


Required Modules
--------------
 - Drupal 7.x 
 - Drupal Core Modules: Search, Path and PHP modules.
 - Drupal contributed modules: Views
 - Database containing GMOD Chado Schema (can be installed by the 
   Tripal Core module)
   
NOTE: A PostgreSQL database is required for installation of the 
Chado Schema

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.