zhxd2/tripal @ 63ed8033a61d44927a08f1163ab1e00813def59b

Sen descrición

Stephen Ficklin 63ed8033a6 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
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=12) %!d(string=hai) anos
tripal_analysis	b1d849910f Renamed analysis API functions back to originals. They got renamed but there was no corresponding deprecated function, plus we will rename them anyway.	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	c1b87f555b Converted old API functions to new functions	%!s(int64=11) %!d(string=hai) anos
tripal_contact	e62ee4cbe7 Fixed permissions -it's hook_permission (not plural) & wasn't implemented consistently as such	%!s(int64=11) %!d(string=hai) anos
tripal_core	aa0f4f7a28 API: tripal_set_message now only shown to uid 1	%!s(int64=11) %!d(string=hai) anos
tripal_cv	ae39e21c8a Renamed include files in cv module. Updated some code in the example modul and added comments to the OBO loader file	%!s(int64=11) %!d(string=hai) anos
tripal_db	a01b1765de DB: cleaned up documentation	%!s(int64=11) %!d(string=hai) anos
tripal_example	ae39e21c8a Renamed include files in cv module. Updated some code in the example modul and added comments to the OBO loader file	%!s(int64=11) %!d(string=hai) anos
tripal_feature	2e42460830 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_featuremap	90f2b33b87 featuremap: cleaned up docs	%!s(int64=11) %!d(string=hai) anos
tripal_genetic	4d9ac83541 Genetic: cleaned up doc	%!s(int64=11) %!d(string=hai) anos
tripal_library	1e024d9bd0 Library: cleaned up doc	%!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity	9862e0d3a8 NatDiv: cleaned up doc	%!s(int64=11) %!d(string=hai) anos
tripal_organism	55882ad802 Organism: cleaned up doc	%!s(int64=11) %!d(string=hai) anos
tripal_phenotype	14ecd9e502 Phenotype: clean up doc	%!s(int64=11) %!d(string=hai) anos
tripal_project	ede5bfaee6 Projects: cleaned up doc	%!s(int64=11) %!d(string=hai) anos
tripal_pub	65ec564a10 Updated documentation for pub module	%!s(int64=11) %!d(string=hai) anos
tripal_stock	f7024f708a Stocks: cleaned up module including documentation and removing no longer used code	%!s(int64=11) %!d(string=hai) anos
tripal_views	84c5a93dab Views: Small tweak to api doc	%!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=12) %!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. 

			
		