zhxd2/tripal @ 913de0f3518e7262ae32cb08cc1e8a808bc276b0

Sen descrición

Stephen Ficklin 913de0f351 Fixed bug that prevented features from being deleted		%!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	f1253790c6 Updates to pub AGL importer and attempts to add code to let user change analysis type (not working yet)	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	798c3edf97 API: Updated bulk loader api to use the new naming rules	%!s(int64=11) %!d(string=hai) anos
tripal_contact	f0a7b4b3a7 Fixed several bugs just by testing	%!s(int64=11) %!d(string=hai) anos
tripal_core	6fb7430c22 Merge branch '7.x-2.x' of git.drupal.org:sandbox/spficklin/1337878 into 7.x-2.x	%!s(int64=11) %!d(string=hai) anos
tripal_cv	913de0f351 Fixed bug that prevented features from being deleted	%!s(int64=11) %!d(string=hai) anos
tripal_db	27587d9d9d Fixed bug with OBO loader, dependency with DB module, and removed the old javascript jsTree library	%!s(int64=11) %!d(string=hai) anos
tripal_example	3f6a5fceac Updated all modules to set default vocabularies	%!s(int64=11) %!d(string=hai) anos
tripal_feature	913de0f351 Fixed bug that prevented features from being deleted	%!s(int64=11) %!d(string=hai) anos
tripal_featuremap	3f6a5fceac Updated all modules to set default vocabularies	%!s(int64=11) %!d(string=hai) anos
tripal_genetic	cac6f2f0cb API: Removed placeholder files	%!s(int64=11) %!d(string=hai) anos
tripal_library	f0a7b4b3a7 Fixed several bugs just by testing	%!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity	cac6f2f0cb API: Removed placeholder files	%!s(int64=11) %!d(string=hai) anos
tripal_organism	3f6a5fceac Updated all modules to set default vocabularies	%!s(int64=11) %!d(string=hai) anos
tripal_phenotype	eb4d880fec Changed all user_access checks to use 'administer tripal' instead of 'access administative pages	%!s(int64=11) %!d(string=hai) anos
tripal_project	93cc0d4349 Project: Fixed bug restricting project relationships to 1 of each type	%!s(int64=11) %!d(string=hai) anos
tripal_pub	f1253790c6 Updates to pub AGL importer and attempts to add code to let user change analysis type (not working yet)	%!s(int64=11) %!d(string=hai) anos
tripal_stock	ed03d02002 Bug Fix: In Stock Organism tpl tried to access nid through stock instead of node	%!s(int64=11) %!d(string=hai) anos
tripal_views	b608951198 API: Updated tripal views api to use new naming rules	%!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. 

			
		