zhxd2/tripal @ ac4f1545e5b8f39f9bd17e04a5680bf2991dff85

Sen descrición

Stephen Ficklin ac4f1545e5 Fixed bug with stock config reseting default vocabs and added documentation to GFF loader function		%!s(int64=11) %!d(string=hai) anos
docs	8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x	%!s(int64=11) %!d(string=hai) anos
tripal_analysis	bb7484a963 Fixes to mviews and custom table API/includes. Still some more fixes to go	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	2d50dc229e Bulk Loader: fixed field adding error and added checking for FALSE template/record/field_id in path	%!s(int64=11) %!d(string=hai) anos
tripal_contact	2c6657d84c Added update functions for custom tables where fK relationships were missing. Fixed other bugs and removed ability to edit legacy MViews	%!s(int64=11) %!d(string=hai) anos
tripal_core	b58fab1d59 Forgot to uncomment the language setting when syncing nodes	%!s(int64=11) %!d(string=hai) anos
tripal_cv	5e82fb32e8 Fixed issues with re-setting Feature URLs and node languages. Also started to fix same for stocks but can't create a stock... need to debug that	%!s(int64=11) %!d(string=hai) anos
tripal_db	3b15f3b503 Nightly checkin .... fixed some issues that caused log entries. working on adding CDS sequences to sequence page	%!s(int64=11) %!d(string=hai) anos
tripal_example	ddf18ece9e Added missing files to example module. Working on default CV form	%!s(int64=11) %!d(string=hai) anos
tripal_feature	ac4f1545e5 Fixed bug with stock config reseting default vocabs and added documentation to GFF loader function	%!s(int64=11) %!d(string=hai) anos
tripal_featuremap	2c6657d84c Added update functions for custom tables where fK relationships were missing. Fixed other bugs and removed ability to edit legacy MViews	%!s(int64=11) %!d(string=hai) anos
tripal_genetic	3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions	%!s(int64=11) %!d(string=hai) anos
tripal_library	bb7484a963 Fixes to mviews and custom table API/includes. Still some more fixes to go	%!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity	3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions	%!s(int64=11) %!d(string=hai) anos
tripal_organism	f9b0f74a0d Fixed an SQL bug that deleting an organism is impossible.	%!s(int64=11) %!d(string=hai) anos
tripal_phenotype	3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions	%!s(int64=11) %!d(string=hai) anos
tripal_project	325a08dce5 Added URL aliasing to projects	%!s(int64=11) %!d(string=hai) anos
tripal_pub	2c6657d84c Added update functions for custom tables where fK relationships were missing. Fixed other bugs and removed ability to edit legacy MViews	%!s(int64=11) %!d(string=hai) anos
tripal_stock	ac4f1545e5 Fixed bug with stock config reseting default vocabs and added documentation to GFF loader function	%!s(int64=11) %!d(string=hai) anos
tripal_views	d61c76ad6e Views Integration: Fixed small bug in UI that didn't handle saving when there were no joins to the current table	%!s(int64=11) %!d(string=hai) anos
.gitignore	455df59fcc removing empty lines	%!s(int64=13) %!d(string=hai) anos
LICENSE.txt	f8f44afa9c Added orphaned form items to sync form. Library module is now converted.	%!s(int64=11) %!d(string=hai) anos
README.txt	8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x	%!s(int64=11) %!d(string=hai) anos

		
			
			
				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 allow anyone 
with genomic data to quickly create an online genomic database using 
community supported tools.


Features
--------------
 - a Chado installer
 - Data loaders for ontologies (controlled vocabularies), GFF files, 
   and FASTA files
 - Generic 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
 - Web pages can be enriched with analysis results from BLAST, 
   KAAS/KEGG, InterProScan, and Gene Ontology (GO)
 - 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 6.x (work is currently underway for a 7.x compatible 
   version)
 - Drupal Core Modules: Search and Path
 - 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

Highly Recommended Modules
 - Views 2.x (Views 3.x compatible version already exists in 6.x-0.4-dev)
 - Views Data Export


Installation
--------------
Please follow the online tutorial for installation instructions:
http://www.gmod.org/wiki/Tripal_Tutorial_v1.1


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.


Future Work
--------------
Currently, Tripal only supports a large subset of the 
current Chado schema, but further development is underway. Meanwhile, 
others can use the Tripal API to develop their own extensions. Those 
extensions can in turn be made available for anyone to use. These 
custom extensions, the Tripal package, and access to support resource 
such as an active mailing list can be found on the Tripal website 
(http://tripal.sourceforge.net).

For more information, see the recent publication:

Stephen P. Ficklin, Lacey-Anne Sanderson, Chun-Huai Cheng, Margaret 
Staton, Taein Lee, Il-Hyung Cho, Sook Jung, Kirstin E Bett, Dorrie 
Main. Tripal: a construction Toolkit for Online Genome Databases. 
Database, Sept 2011. Vol 2011. 

			
		