zhxd2/tripal @ 3e6666284dcd832dd5a7926fb40341822c7139e1

Sen descrición

Stephen Ficklin 3e6666284d Updated documentation for feature sequences		%!s(int64=10) %!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	e5370d767c Chado Node API: Added the ability to set titles to all node types :)	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	2d50dc229e Bulk Loader: fixed field adding error and added checking for FALSE template/record/field_id in path	%!s(int64=11) %!d(string=hai) anos
tripal_contact	e5370d767c Chado Node API: Added the ability to set titles to all node types :)	%!s(int64=11) %!d(string=hai) anos
tripal_core	f6ea56ac65 Small fixes to the node title api	%!s(int64=10) %!d(string=hai) anos
tripal_cv	138b11d0ce Various bug fixes realated to printing errors after rolling back transactions. Fixed issue with OBO parser not having a default CV and a few others	%!s(int64=10) %!d(string=hai) anos
tripal_db	3b15f3b503 Nightly checkin .... fixed some issues that caused log entries. working on adding CDS sequences to sequence page	%!s(int64=11) %!d(string=hai) anos
tripal_example	138b11d0ce Various bug fixes realated to printing errors after rolling back transactions. Fixed issue with OBO parser not having a default CV and a few others	%!s(int64=10) %!d(string=hai) anos
tripal_feature	3e6666284d Updated documentation for feature sequences	%!s(int64=10) %!d(string=hai) anos
tripal_featuremap	e5370d767c Chado Node API: Added the ability to set titles to all node types :)	%!s(int64=11) %!d(string=hai) anos
tripal_genetic	3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions	%!s(int64=11) %!d(string=hai) anos
tripal_library	e5370d767c Chado Node API: Added the ability to set titles to all node types :)	%!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity	3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions	%!s(int64=11) %!d(string=hai) anos
tripal_organism	e5370d767c Chado Node API: Added the ability to set titles to all node types :)	%!s(int64=11) %!d(string=hai) anos
tripal_phenotype	3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions	%!s(int64=11) %!d(string=hai) anos
tripal_project	e5370d767c Chado Node API: Added the ability to set titles to all node types :)	%!s(int64=11) %!d(string=hai) anos
tripal_pub	138b11d0ce Various bug fixes realated to printing errors after rolling back transactions. Fixed issue with OBO parser not having a default CV and a few others	%!s(int64=10) %!d(string=hai) anos
tripal_stock	ba48682fb9 Chado Node API: cleaned up the set title code and added the ability for modules to set a default for their content type	%!s(int64=11) %!d(string=hai) anos
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	%!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. 

			
		