zhxd2/tripal @ e8ff2cc7c03d01bdac3024c7e24b0e887967277a

Sen descrición

Stephen Ficklin e8ff2cc7c0 Fixed bug in organism_stock template when no stocks are synced		%!s(int64=10) %!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	5096765d58 few minor bug fixes, additions to CS	%!s(int64=10) %!d(string=hai) anos
tripal_bulk_loader	6a812e5652 Switch #markup to #theme & #node in hook_node_view() to ensure that pages are not rendered ahead of time allowing modules to modify the panes being rendered	%!s(int64=10) %!d(string=hai) anos
tripal_contact	6a812e5652 Switch #markup to #theme & #node in hook_node_view() to ensure that pages are not rendered ahead of time allowing modules to modify the panes being rendered	%!s(int64=10) %!d(string=hai) anos
tripal_core	a5feceb743 Added support for Tripal variables by adding a new API. Added limit and offset to chado_select_record()	%!s(int64=10) %!d(string=hai) anos
tripal_cv	6230b71886 Changed package to 'tripal' for all modules	%!s(int64=10) %!d(string=hai) anos
tripal_db	6230b71886 Changed package to 'tripal' for all modules	%!s(int64=10) %!d(string=hai) anos
tripal_example	6a812e5652 Switch #markup to #theme & #node in hook_node_view() to ensure that pages are not rendered ahead of time allowing modules to modify the panes being rendered	%!s(int64=10) %!d(string=hai) anos
tripal_feature	5096765d58 few minor bug fixes, additions to CS	%!s(int64=10) %!d(string=hai) anos
tripal_featuremap	5096765d58 few minor bug fixes, additions to CS	%!s(int64=10) %!d(string=hai) anos
tripal_genetic	6f22290db5 Missed non-node hook_view_node implementations: now switched to #theme as well	%!s(int64=10) %!d(string=hai) anos
tripal_library	762165d116 Fixed type	%!s(int64=10) %!d(string=hai) anos
tripal_natural_diversity	6f22290db5 Missed non-node hook_view_node implementations: now switched to #theme as well	%!s(int64=10) %!d(string=hai) anos
tripal_organism	a5feceb743 Added support for Tripal variables by adding a new API. Added limit and offset to chado_select_record()	%!s(int64=10) %!d(string=hai) anos
tripal_phenotype	6f22290db5 Missed non-node hook_view_node implementations: now switched to #theme as well	%!s(int64=10) %!d(string=hai) anos
tripal_project	5d51137e57 Fixed bug in code with template variables	%!s(int64=10) %!d(string=hai) anos
tripal_pub	22f047130d Fixed an error showing on the pub search	%!s(int64=10) %!d(string=hai) anos
tripal_stock	e8ff2cc7c0 Fixed bug in organism_stock template when no stocks are synced	%!s(int64=10) %!d(string=hai) anos
tripal_views	cc3ce5973e Small fix to tripal views chado integrations: ensured that field description is properly set even if not specified in the schema api	%!s(int64=10) %!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. 

			
		