zhxd2/tripal @ d502001c0d23c4111a3919525b9ff4761f58f01b

Geen omschrijving

Lacey Sanderson d502001c0d Small fix to drush re-run command to take into account the function name changes		12 jaren geleden
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	12 jaren geleden
tripal_bulk_loader	82a8225193 Small fix to bulk loader drush revert command	12 jaren geleden
tripal_contact	cd87d5a56a Fixed Drupal formatting standards	12 jaren geleden
tripal_core	d502001c0d Small fix to drush re-run command to take into account the function name changes	12 jaren geleden
tripal_cv	8098c77257 Fixed memory leaks in OBO loader.	12 jaren geleden
tripal_db	42fe28540f Fixed issue #1712422. Changed all Chado querie to use chado_query() rather than db_query()	12 jaren geleden
tripal_feature	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	12 jaren geleden
tripal_featuremap	9bb94c3748 Fixed issue #1699022. Took out all code that tried to distinguish a revision.	12 jaren geleden
tripal_genetic	cd87d5a56a Fixed Drupal formatting standards	12 jaren geleden
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	12 jaren geleden
tripal_natural_diversity	cd87d5a56a Fixed Drupal formatting standards	12 jaren geleden
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	12 jaren geleden
tripal_phenotype	cd87d5a56a Fixed Drupal formatting standards	12 jaren geleden
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	12 jaren geleden
tripal_stock	fb03c073df Added a stock api function to mimic sync'ing in other chado modules	12 jaren geleden
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 jaren geleden
.gitignore	455df59fcc removing empty lines	13 jaren geleden
README.txt	a2d10bc7f7 Added describptive README and removed LISCENSE	12 jaren geleden

		
			
			
				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.

			
		