Updated README

README.md

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+# About
+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: 
+
+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
+* 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.