zhxd2/tripal @ 66ef98e133afee99069d80a2fafc6685754b4e9e

Sen descrición

spficklin 66ef98e133 Fixed tripal db module to use Tripal API, adjusted the help text, validates if database name already exists before trying to add/edit. And added checks in tripal core select/insert/update/delete functions to make sure and arguments are arrays and they have values		%!s(int64=12) %!d(string=hai) anos
tripal_analysis	614de6fb7e Removed Published Node filter from default views to reduce confusion over -I loaded some features but they don't show up in the feature listing; because they're not yet sync'd	%!s(int64=12) %!d(string=hai) anos
tripal_bulk_loader	82a8225193 Small fix to bulk loader drush revert command	%!s(int64=12) %!d(string=hai) anos
tripal_contact	cd87d5a56a Fixed Drupal formatting standards	%!s(int64=12) %!d(string=hai) anos
tripal_core	66ef98e133 Fixed tripal db module to use Tripal API, adjusted the help text, validates if database name already exists before trying to add/edit. And added checks in tripal core select/insert/update/delete functions to make sure and arguments are arrays and they have values	%!s(int64=12) %!d(string=hai) anos
tripal_cv	8098c77257 Fixed memory leaks in OBO loader.	%!s(int64=12) %!d(string=hai) anos
tripal_db	66ef98e133 Fixed tripal db module to use Tripal API, adjusted the help text, validates if database name already exists before trying to add/edit. And added checks in tripal core select/insert/update/delete functions to make sure and arguments are arrays and they have values	%!s(int64=12) %!d(string=hai) anos
tripal_feature	d7e679c118 Removed match_part from parent/child variables in the alignment preprocess function	%!s(int64=12) %!d(string=hai) anos
tripal_featuremap	9bb94c3748 Fixed issue #1699022. Took out all code that tried to distinguish a revision.	%!s(int64=12) %!d(string=hai) anos
tripal_genetic	cd87d5a56a Fixed Drupal formatting standards	%!s(int64=12) %!d(string=hai) anos
tripal_library	614de6fb7e Removed Published Node filter from default views to reduce confusion over -I loaded some features but they don't show up in the feature listing; because they're not yet sync'd	%!s(int64=12) %!d(string=hai) anos
tripal_natural_diversity	cd87d5a56a Fixed Drupal formatting standards	%!s(int64=12) %!d(string=hai) anos
tripal_organism	614de6fb7e Removed Published Node filter from default views to reduce confusion over -I loaded some features but they don't show up in the feature listing; because they're not yet sync'd	%!s(int64=12) %!d(string=hai) anos
tripal_phenotype	cd87d5a56a Fixed Drupal formatting standards	%!s(int64=12) %!d(string=hai) anos
tripal_project	614de6fb7e Removed Published Node filter from default views to reduce confusion over -I loaded some features but they don't show up in the feature listing; because they're not yet sync'd	%!s(int64=12) %!d(string=hai) anos
tripal_stock	fb03c073df Added a stock api function to mimic sync'ing in other chado modules	%!s(int64=12) %!d(string=hai) anos
tripal_views	a2b1e53694 Added a new 'Create New Integration' checkbox to the tripal views integration to allow users to create new integrations based off of default ones. Also set defaults so that a new integration is created when the original integration priority was 10 or 9 and added form validation to ensure that users don't save views with a priority of 10 or 9	%!s(int64=12) %!d(string=hai) anos
.gitignore	455df59fcc removing empty lines	%!s(int64=13) %!d(string=hai) anos
README.txt	a2d10bc7f7 Added describptive README and removed LISCENSE	%!s(int64=12) %!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.

			
		