zhxd2/tripal @ 1706616450adc8969fb796b8a00bc125a78d38ae

Sen descrición

Lacey Sanderson 1706616450 API: changed [table]_retrieve to chado_[table]_retrieve		%!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	1706616450 API: changed [table]_retrieve to chado_[table]_retrieve	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	4ceabfdb8e Fixed formatting issues with templates and adjusted comment in hook_update_N to remove @ingroup tags as those show up when drush updatedb is run	%!s(int64=11) %!d(string=hai) anos
tripal_contact	38c845af5a API: changed [table]_insert to chado_[table]_insert_record to fix conflict with drupal's db_insert	%!s(int64=11) %!d(string=hai) anos
tripal_core	38d6b34898 Fixed merge conflicts	%!s(int64=11) %!d(string=hai) anos
tripal_cv	1706616450 API: changed [table]_retrieve to chado_[table]_retrieve	%!s(int64=11) %!d(string=hai) anos
tripal_db	1706616450 API: changed [table]_retrieve to chado_[table]_retrieve	%!s(int64=11) %!d(string=hai) anos
tripal_example	283f42f54c Fixed problem with hook_node_access functions denying all pages	%!s(int64=11) %!d(string=hai) anos
tripal_feature	19137be811 Updated API to use new function names	%!s(int64=11) %!d(string=hai) anos
tripal_featuremap	19137be811 Updated API to use new function names	%!s(int64=11) %!d(string=hai) anos
tripal_genetic	cac6f2f0cb API: Removed placeholder files	%!s(int64=11) %!d(string=hai) anos
tripal_library	76f90b145f API: set deprecated messages to have a module of tripal_deprecated to make it easy to filter these notices out	%!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity	cac6f2f0cb API: Removed placeholder files	%!s(int64=11) %!d(string=hai) anos
tripal_organism	1706616450 API: changed [table]_retrieve to chado_[table]_retrieve	%!s(int64=11) %!d(string=hai) anos
tripal_phenotype	eb4d880fec Changed all user_access checks to use 'administer tripal' instead of 'access administative pages	%!s(int64=11) %!d(string=hai) anos
tripal_project	76f90b145f API: set deprecated messages to have a module of tripal_deprecated to make it easy to filter these notices out	%!s(int64=11) %!d(string=hai) anos
tripal_pub	38d6b34898 Fixed merge conflicts	%!s(int64=11) %!d(string=hai) anos
tripal_stock	1706616450 API: changed [table]_retrieve to chado_[table]_retrieve	%!s(int64=11) %!d(string=hai) anos
tripal_views	4ceabfdb8e Fixed formatting issues with templates and adjusted comment in hook_update_N to remove @ingroup tags as those show up when drush updatedb is run	%!s(int64=11) %!d(string=hai) anos
.gitignore	455df59fcc removing empty lines	%!s(int64=13) %!d(string=hai) anos
LICENSE.txt	f8f44afa9c Added orphaned form items to sync form. Library module is now converted.	%!s(int64=11) %!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. 

			
		