zhxd2/tripal @ a47af35a267b2fa65e51faf82a4e6ee055b703c7

Sen descrición

1983 Achegas

Lacey Sanderson a47af35a26 API: Moved prop/dbxref/relationship APIs to the tripal_api module and added wrappers. Original code is still in tripal_core but not included		%!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	df26ed8bea Stock templates converted. Fixed some other templates	%!s(int64=11) %!d(string=hai) anos
tripal_api	a47af35a26 API: Moved prop/dbxref/relationship APIs to the tripal_api module and added wrappers. Original code is still in tripal_core but not included	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module	%!s(int64=11) %!d(string=hai) anos
tripal_contact	49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module	%!s(int64=11) %!d(string=hai) anos
tripal_core	a47af35a26 API: Moved prop/dbxref/relationship APIs to the tripal_api module and added wrappers. Original code is still in tripal_core but not included	%!s(int64=11) %!d(string=hai) anos
tripal_cv	49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module	%!s(int64=11) %!d(string=hai) anos
tripal_db	49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module	%!s(int64=11) %!d(string=hai) anos
tripal_example	db8b355873 Made a bug fix to the feature module. Included documentation in the tripal_example.chado_node.inc file	%!s(int64=11) %!d(string=hai) anos
tripal_feature	df26ed8bea Stock templates converted. Fixed some other templates	%!s(int64=11) %!d(string=hai) anos
tripal_featuremap	15cf37dff9 Project module is converted. Added publication templates to library, stock and feature	%!s(int64=11) %!d(string=hai) anos
tripal_genetic	4b664d7114 ND module done... will need more testing with large dataset	%!s(int64=11) %!d(string=hai) anos
tripal_library	49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module	%!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity	2cedc4943b Fixed bug in stock module that made genotypes show up twice	%!s(int64=11) %!d(string=hai) anos
tripal_organism	2cedc4943b Fixed bug in stock module that made genotypes show up twice	%!s(int64=11) %!d(string=hai) anos
tripal_phenotype	8bd0b15d71 Fixed phenotype module to include the tripal_feature.phenotype.tpl.php template	%!s(int64=11) %!d(string=hai) anos
tripal_project	df26ed8bea Stock templates converted. Fixed some other templates	%!s(int64=11) %!d(string=hai) anos
tripal_pub	996d6c0c1d Added an example module to serve as a template for anyone who wants to create an extension module. It will eventually have stubs for all functions	%!s(int64=11) %!d(string=hai) anos
tripal_stock	df26ed8bea Stock templates converted. Fixed some other templates	%!s(int64=11) %!d(string=hai) anos
tripal_views	49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module	%!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. 

			
		