zhxd2/tripal @ 91c0e33ad98726f92021e9b2efaab0fa9fdd2db3

Sen descrición

1998 Achegas

Lacey Sanderson 91c0e33ad9 API: Added Additional documentation to the various core chado api		%!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	abe60dfdfb MViews no longer get removed on module uninstall	%!s(int64=11) %!d(string=hai) anos
tripal_api	b2d20ff7b2 API: Removed api module and re-instated the tripal_core dbxref/relationship apis, moved the new properties api into the tripal_core.properties.api.inc file with yet again new names. Not backwards compatible	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module	%!s(int64=11) %!d(string=hai) anos
tripal_contact	ff84d63214 API: Split up massive chado api into multiple files and re-named all core api files to be consistent	%!s(int64=11) %!d(string=hai) anos
tripal_core	91c0e33ad9 API: Added Additional documentation to the various core chado api	%!s(int64=11) %!d(string=hai) anos
tripal_cv	abe60dfdfb MViews no longer get removed on module uninstall	%!s(int64=11) %!d(string=hai) anos
tripal_db	49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module	%!s(int64=11) %!d(string=hai) anos
tripal_example	0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done	%!s(int64=11) %!d(string=hai) anos
tripal_feature	abe60dfdfb MViews no longer get removed on module uninstall	%!s(int64=11) %!d(string=hai) anos
tripal_featuremap	571c4d5db3 Updated analysis, contact, featuremap, project, pub and stock to use the new properties api	%!s(int64=11) %!d(string=hai) anos
tripal_genetic	4b664d7114 ND module done... will need more testing with large dataset	%!s(int64=11) %!d(string=hai) anos
tripal_library	abe60dfdfb MViews no longer get removed on module uninstall	%!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity	2cedc4943b Fixed bug in stock module that made genotypes show up twice	%!s(int64=11) %!d(string=hai) anos
tripal_organism	0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done	%!s(int64=11) %!d(string=hai) anos
tripal_phenotype	8bd0b15d71 Fixed phenotype module to include the tripal_feature.phenotype.tpl.php template	%!s(int64=11) %!d(string=hai) anos
tripal_project	571c4d5db3 Updated analysis, contact, featuremap, project, pub and stock to use the new properties api	%!s(int64=11) %!d(string=hai) anos
tripal_pub	ff84d63214 API: Split up massive chado api into multiple files and re-named all core api files to be consistent	%!s(int64=11) %!d(string=hai) anos
tripal_stock	1013abb11c Bug fixes to dbxref/prop/rel api	%!s(int64=11) %!d(string=hai) anos
tripal_views	49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module	%!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. 

			
		