zhxd2/tripal @ 0e4a26e1fc5450c4a8ecbea40f1665571afe95fc

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Stephen Ficklin 0e4a26e1fc Changed bulk loader theming to match new Tripal style		преди 10 години
docs	8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x	преди 11 години
tripal_analysis	e86f0491d8 Fixed bug in Title/Path API: insert and update hooks didn't have the table object which required that the form field ids matched table names. This can't always be guaranteed	преди 10 години
tripal_bulk_loader	0e4a26e1fc Changed bulk loader theming to match new Tripal style	преди 10 години
tripal_contact	e86f0491d8 Fixed bug in Title/Path API: insert and update hooks didn't have the table object which required that the form field ids matched table names. This can't always be guaranteed	преди 10 години
tripal_core	0e4a26e1fc Changed bulk loader theming to match new Tripal style	преди 10 години
tripal_cv	d4b0a1eb19 Made documentation changes to Titles & Path API	преди 10 години
tripal_db	3b15f3b503 Nightly checkin .... fixed some issues that caused log entries. working on adding CDS sequences to sequence page	преди 11 години
tripal_example	e86f0491d8 Fixed bug in Title/Path API: insert and update hooks didn't have the table object which required that the form field ids matched table names. This can't always be guaranteed	преди 10 години
tripal_feature	23803436fd Fixed bug in feature summary table	преди 10 години
tripal_featuremap	e86f0491d8 Fixed bug in Title/Path API: insert and update hooks didn't have the table object which required that the form field ids matched table names. This can't always be guaranteed	преди 10 години
tripal_genetic	3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions	преди 11 години
tripal_library	e86f0491d8 Fixed bug in Title/Path API: insert and update hooks didn't have the table object which required that the form field ids matched table names. This can't always be guaranteed	преди 10 години
tripal_natural_diversity	3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions	преди 11 години
tripal_organism	e86f0491d8 Fixed bug in Title/Path API: insert and update hooks didn't have the table object which required that the form field ids matched table names. This can't always be guaranteed	преди 10 години
tripal_phenotype	3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions	преди 11 години
tripal_project	e86f0491d8 Fixed bug in Title/Path API: insert and update hooks didn't have the table object which required that the form field ids matched table names. This can't always be guaranteed	преди 10 години
tripal_pub	c8fec206bb Fixed bugs with pub module and feature module	преди 10 години
tripal_stock	e86f0491d8 Fixed bug in Title/Path API: insert and update hooks didn't have the table object which required that the form field ids matched table names. This can't always be guaranteed	преди 10 години
tripal_views	fa1525e439 Views: Added a generic select list by ID filter handler which works on any foreign key as long as the referenced table has a name field	преди 11 години
.gitignore	455df59fcc removing empty lines	преди 13 години
LICENSE.txt	f8f44afa9c Added orphaned form items to sync form. Library module is now converted.	преди 11 години
README.txt	8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x	преди 11 години

		
			
			
				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. 

			
		