zhxd2/tripal @ 424a6bca6ae4026de2d25e8063d63e2d2bba99d6

Sen descrición

spficklin 424a6bca6a Fixing merge conflict with tripal_views		%!s(int64=13) %!d(string=hai) anos
tripal_analysis	51e6d550ea Fixed hard-coded handler names that changed from chado_ to tripal_	%!s(int64=13) %!d(string=hai) anos
tripal_bulk_loader	9fb12a9da3 Fixed bulk loader to use is_prepared rather then prepare since the tripal_core_chado_insert has changed	%!s(int64=13) %!d(string=hai) anos
tripal_contact	66b9cfc511 Created contact, genetic and project default views	%!s(int64=13) %!d(string=hai) anos
tripal_core	5816ad9df7 added a field and filter handler for a sequence. Also fixed a fwe butgs in the gff loader, added a new function in the feature API for generating a reverse compliment	%!s(int64=13) %!d(string=hai) anos
tripal_cv	1f6ad0c3af Simple default fixes to the cv, db and feature default views	%!s(int64=13) %!d(string=hai) anos
tripal_db	1f6ad0c3af Simple default fixes to the cv, db and feature default views	%!s(int64=13) %!d(string=hai) anos
tripal_feature	424a6bca6a Fixing merge conflict with tripal_views	%!s(int64=13) %!d(string=hai) anos
tripal_genetic	d7526c32fe Small fixes to genetic, library, natural diversity, phenotype, project and stock default views	%!s(int64=13) %!d(string=hai) anos
tripal_library	d7526c32fe Small fixes to genetic, library, natural diversity, phenotype, project and stock default views	%!s(int64=13) %!d(string=hai) anos
tripal_natural_diversity	d7526c32fe Small fixes to genetic, library, natural diversity, phenotype, project and stock default views	%!s(int64=13) %!d(string=hai) anos
tripal_organism	51e6d550ea Fixed hard-coded handler names that changed from chado_ to tripal_	%!s(int64=13) %!d(string=hai) anos
tripal_phenotype	d7526c32fe Small fixes to genetic, library, natural diversity, phenotype, project and stock default views	%!s(int64=13) %!d(string=hai) anos
tripal_project	d7526c32fe Small fixes to genetic, library, natural diversity, phenotype, project and stock default views	%!s(int64=13) %!d(string=hai) anos
tripal_stock	d7526c32fe Small fixes to genetic, library, natural diversity, phenotype, project and stock default views	%!s(int64=13) %!d(string=hai) anos
tripal_views	424a6bca6a Fixing merge conflict with tripal_views	%!s(int64=13) %!d(string=hai) anos
.gitignore	455df59fcc removing empty lines	%!s(int64=14) %!d(string=hai) anos
README.txt	a2d10bc7f7 Added describptive README and removed LISCENSE	%!s(int64=13) %!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
1. Enable/Install the Tripal Core Module
2. Install a Chado database
     - Either allow Tripal to add a chado database in a separate 
       schema to your Drupal database (recommended) by navigating to 
       Administer -> Tripal Management -> Install Chado 
       (admin/tripal/chado_1_11_install) and click "Install Chado" OR
     - Edit the settings.php file to connect to an external chado 
       database
3. Enable/Install any other Tripal modules that are applicable to 
   your site.
4. Check the module page for each enabled Tripal module for further 
   module-specific instructions and a list of features and quick 
   links (Administer -> Tripal Managment -> [Module Name]

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 visualization of a 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.

			
		