zhxd2/tripal @ f429f288c4300dbb604f74232524d615c0bb29e9

Sen descrición

Lacey Sanderson f429f288c4 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=11) %!d(string=hai) anos
tripal_analysis	4dfd3d859b Continued coversion of analysis, organism, project and feature modules	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	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_contact	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_core	d922b7a57b Fixed minor coding review problems	%!s(int64=11) %!d(string=hai) anos
tripal_cv	d922b7a57b Fixed minor coding review problems	%!s(int64=11) %!d(string=hai) anos
tripal_db	d922b7a57b Fixed minor coding review problems	%!s(int64=11) %!d(string=hai) anos
tripal_feature	4dfd3d859b Continued coversion of analysis, organism, project and feature modules	%!s(int64=11) %!d(string=hai) anos
tripal_featuremap	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_genetic	fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed	%!s(int64=11) %!d(string=hai) anos
tripal_library	69e0f8271f Merge branch '6.x-1.x' into 7.x-2.x	%!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity	a59bff7fee Commented out ND default view	%!s(int64=11) %!d(string=hai) anos
tripal_organism	4dfd3d859b Continued coversion of analysis, organism, project and feature modules	%!s(int64=11) %!d(string=hai) anos
tripal_phenotype	fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed	%!s(int64=11) %!d(string=hai) anos
tripal_project	4dfd3d859b Continued coversion of analysis, organism, project and feature modules	%!s(int64=11) %!d(string=hai) anos
tripal_pub	69e0f8271f Merge branch '6.x-1.x' into 7.x-2.x	%!s(int64=11) %!d(string=hai) anos
tripal_stock	69e0f8271f Merge branch '6.x-1.x' into 7.x-2.x	%!s(int64=11) %!d(string=hai) anos
tripal_views	e6289bd103 Tripal Views: Updates to integration edit form to make it work with Drupal 7. Ajax for the join fields still not working.	%!s(int64=11) %!d(string=hai) anos
.gitignore	455df59fcc removing empty lines	%!s(int64=13) %!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. 

			
		