zhxd2/tripal @ 1097f37112296eb577d6aefcf758efce75622976

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spficklin 1097f37112 Fixed typo in require		12 年之前
tripal_analysis	fb42852fa2 Reorganization of functions into api, includes and theme files to make all modules consistent	12 年之前
tripal_bulk_loader	82a8225193 Small fix to bulk loader drush revert command	12 年之前
tripal_contact	d2b7b59b9e Fixed issues with the library module	12 年之前
tripal_core	fb42852fa2 Reorganization of functions into api, includes and theme files to make all modules consistent	12 年之前
tripal_cv	b6444c78ad Debugging Tripal CV module and created API function for feature relationships	12 年之前
tripal_db	fb42852fa2 Reorganization of functions into api, includes and theme files to make all modules consistent	12 年之前
tripal_feature	9964a101c6 Removed preprocess function that accidentally got incorporated but was for a custom site. Also removed api function in organism module that didn't fit	12 年之前
tripal_featuremap	fb42852fa2 Reorganization of functions into api, includes and theme files to make all modules consistent	12 年之前
tripal_genetic	1097f37112 Fixed typo in require	12 年之前
tripal_library	fb42852fa2 Reorganization of functions into api, includes and theme files to make all modules consistent	12 年之前
tripal_natural_diversity	fb42852fa2 Reorganization of functions into api, includes and theme files to make all modules consistent	12 年之前
tripal_organism	9964a101c6 Removed preprocess function that accidentally got incorporated but was for a custom site. Also removed api function in organism module that didn't fit	12 年之前
tripal_phenotype	cd87d5a56a Fixed Drupal formatting standards	12 年之前
tripal_project	fb42852fa2 Reorganization of functions into api, includes and theme files to make all modules consistent	12 年之前
tripal_stock	9964a101c6 Removed preprocess function that accidentally got incorporated but was for a custom site. Also removed api function in organism module that didn't fit	12 年之前
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	12 年之前
.gitignore	455df59fcc removing empty lines	13 年之前
README.txt	a2d10bc7f7 Added describptive README and removed LISCENSE	12 年之前

		
			
			
				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.

			
		