zhxd2/tripal @ 6.x-1.x

No Description

Ficklin f3f17b6ec1 Fixed merge conflict		9 years ago
docs	dd6d29004d Fixed size limit in pub importer text field. Updated doxygen config file	11 years ago
tripal_analysis	1b513eb0fb Small bug fixes	10 years ago
tripal_bulk_loader	24cf39f91b added template for the organism references, anf fixed obo loader when missing default namespace	10 years ago
tripal_contact	3388ff58d8 Various bug fixes discovered in the process of converting to Drupal 7	10 years ago
tripal_core	2fa23ec5b4 bug fixes for strict PHP	10 years ago
tripal_cv	24cf39f91b added template for the organism references, anf fixed obo loader when missing default namespace	10 years ago
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	11 years ago
tripal_feature	f3f17b6ec1 Fixed merge conflict	9 years ago
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	11 years ago
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	11 years ago
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.	11 years ago
tripal_natural_diversity	0c408f3863 Added chado eimage node type (in a new Tripal Eimage module) and chado nd_geolocation node type (in Tripal Natural Diversity module)	10 years ago
tripal_organism	24cf39f91b added template for the organism references, anf fixed obo loader when missing default namespace	10 years ago
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	11 years ago
tripal_project	87e6c5f4bf Removed the listing of all images for the sync admin interface.	10 years ago
tripal_pub	36bd0104f8 Fix for AGL importer	10 years ago
tripal_stock	20731f50b9 Added check for length of URL exceeding 128 chars	11 years ago
tripal_views	3388ff58d8 Various bug fixes discovered in the process of converting to Drupal 7	10 years ago
.gitignore	455df59fcc removing empty lines	13 years ago
LICENSE.txt	3388ff58d8 Various bug fixes discovered in the process of converting to Drupal 7	10 years ago
README.txt	9c0fdf6d45 Tripal release v1.1 - 2013/06/24	11 years ago

		
			
			
				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. 

			
		