zhxd2/tripal @ 77e5587088759e1abc9aea80cf76857f742d0187

Sen descrición

Stephen Ficklin 77e5587088 Fixed bug with seqlen calcuation after importing FASTA. Fixed bug in duplicates of OBO loaders and updated to support relative paths		%!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	141b6d0654 updated property API calls	%!s(int64=10) %!d(string=hai) anos
tripal_bulk_loader	db0da648ee Fixed issues with error reporting in bulk loader, and warnings when syncing organisms	%!s(int64=10) %!d(string=hai) anos
tripal_contact	77e5587088 Fixed bug with seqlen calcuation after importing FASTA. Fixed bug in duplicates of OBO loaders and updated to support relative paths	%!s(int64=10) %!d(string=hai) anos
tripal_core	b816846340 fixed bugs with updated property API funcs	%!s(int64=10) %!d(string=hai) anos
tripal_cv	77e5587088 Fixed bug with seqlen calcuation after importing FASTA. Fixed bug in duplicates of OBO loaders and updated to support relative paths	%!s(int64=10) %!d(string=hai) anos
tripal_db	141b6d0654 updated property API calls	%!s(int64=10) %!d(string=hai) anos
tripal_example	9017e633ed Fixed bug in stock syncing. Added comments to all hook_node_presave() to prevent the bug from happening again	%!s(int64=10) %!d(string=hai) anos
tripal_feature	77e5587088 Fixed bug with seqlen calcuation after importing FASTA. Fixed bug in duplicates of OBO loaders and updated to support relative paths	%!s(int64=10) %!d(string=hai) anos
tripal_featuremap	141b6d0654 updated property API calls	%!s(int64=10) %!d(string=hai) anos
tripal_genetic	ed694de0f4 Removing TRIPAL VIEWS Deprecated functions	%!s(int64=10) %!d(string=hai) anos
tripal_library	141b6d0654 updated property API calls	%!s(int64=10) %!d(string=hai) anos
tripal_natural_diversity	257ae5eaa6 API Update: updated all modules to use the Analysis, Bulk Loader & Contact APIs	%!s(int64=10) %!d(string=hai) anos
tripal_organism	141b6d0654 updated property API calls	%!s(int64=10) %!d(string=hai) anos
tripal_phenotype	ed694de0f4 Removing TRIPAL VIEWS Deprecated functions	%!s(int64=10) %!d(string=hai) anos
tripal_project	141b6d0654 updated property API calls	%!s(int64=10) %!d(string=hai) anos
tripal_pub	77e5587088 Fixed bug with seqlen calcuation after importing FASTA. Fixed bug in duplicates of OBO loaders and updated to support relative paths	%!s(int64=10) %!d(string=hai) anos
tripal_stock	141b6d0654 updated property API calls	%!s(int64=10) %!d(string=hai) anos
tripal_views	e5698c30ef Applied patch provided by Nelson Nazzicari for the views page listing	%!s(int64=10) %!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. 

			
		