zhxd2/tripal @ c5a88c42f05199e12368f19ea6986072f42ba2f9

Sen descrición

spficklin c5a88c42f0 minor text changes		%!s(int64=11) %!d(string=hai) anos
docs	dd6d29004d Fixed size limit in pub importer text field. Updated doxygen config file	%!s(int64=11) %!d(string=hai) anos
tripal_analysis	98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	587f5f0d42 Reorganized bulk loaer module directory structure to match other Tripal modules and removed setup instructions on admin page as they were incorrect	%!s(int64=11) %!d(string=hai) anos
tripal_contact	98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set	%!s(int64=11) %!d(string=hai) anos
tripal_core	1f8e28c555 added fclose to file_upload_combo, and added form_state variable to ahah_prepare_form function	%!s(int64=11) %!d(string=hai) anos
tripal_cv	587f5f0d42 Reorganized bulk loaer module directory structure to match other Tripal modules and removed setup instructions on admin page as they were incorrect	%!s(int64=11) %!d(string=hai) anos
tripal_db	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_feature	c5a88c42f0 minor text changes	%!s(int64=11) %!d(string=hai) anos
tripal_featuremap	98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set	%!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	ff37627b86 Added ability to set URLs for stocks. Added ability to configure format of stock and feature page titles. Changed the stock syncing to match that of features. Removed the ability to set the title for stocks and features. Titles get set automatically now.	%!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	ff37627b86 Added ability to set URLs for stocks. Added ability to configure format of stock and feature page titles. Changed the stock syncing to match that of features. Removed the ability to set the title for stocks and features. Titles get set automatically now.	%!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	98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set	%!s(int64=11) %!d(string=hai) anos
tripal_pub	a91efd349f Altered directory structure of Tripal views module to match others. Fixed links on admin instruction page for Tripal Views	%!s(int64=11) %!d(string=hai) anos
tripal_stock	c5a88c42f0 minor text changes	%!s(int64=11) %!d(string=hai) anos
tripal_views	a91efd349f Altered directory structure of Tripal views module to match others. Fixed links on admin instruction page for Tripal Views	%!s(int64=11) %!d(string=hai) anos
.gitignore	455df59fcc removing empty lines	%!s(int64=13) %!d(string=hai) anos
README.txt	9c0fdf6d45 Tripal release v1.1 - 2013/06/24	%!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. 

			
		