zhxd2/tripal @ 27dadbfc370c49fcfabd603a8d2e05167d065071

Bez popisu

Stephen Ficklin 27dadbfc37 Removed requirement to have a 'comment' in the views integration import		před 12 roky
tripal_analysis	2840b98e85 All node types (except stock) have a function to cleanup orphaned nodes but it wasn't complete for some. A new core API function was created that all modules with node types can use to clean up orphaned nodes. Also, the drush trpjob-run command was fixed so that a username must be provided to run the job	před 12 roky
tripal_bulk_loader	f627849b77 Fixed memory leaks	před 12 roky
tripal_contact	1e485a0763 Added check to modules to only add default view if tripal_views is enabled -fixes bug of broken views if tripal_views is not enabled	před 12 roky
tripal_core	f627849b77 Fixed memory leaks	před 12 roky
tripal_cv	b55ac8b12f Fixing GO charts	před 12 roky
tripal_db	79368506ed Removed print for dbxref api that was causing WSOD	před 12 roky
tripal_feature	2840b98e85 All node types (except stock) have a function to cleanup orphaned nodes but it wasn't complete for some. A new core API function was created that all modules with node types can use to clean up orphaned nodes. Also, the drush trpjob-run command was fixed so that a username must be provided to run the job	před 12 roky
tripal_genetic	1e485a0763 Added check to modules to only add default view if tripal_views is enabled -fixes bug of broken views if tripal_views is not enabled	před 12 roky
tripal_library	9403a5867d Removed old menu option from library configuration page	před 12 roky
tripal_natural_diversity	1e485a0763 Added check to modules to only add default view if tripal_views is enabled -fixes bug of broken views if tripal_views is not enabled	před 12 roky
tripal_organism	2840b98e85 All node types (except stock) have a function to cleanup orphaned nodes but it wasn't complete for some. A new core API function was created that all modules with node types can use to clean up orphaned nodes. Also, the drush trpjob-run command was fixed so that a username must be provided to run the job	před 12 roky
tripal_phenotype	e1fba05c06 Made all messages for no results be consistent for all default views	před 12 roky
tripal_project	e1fba05c06 Made all messages for no results be consistent for all default views	před 12 roky
tripal_stock	e1fba05c06 Made all messages for no results be consistent for all default views	před 12 roky
tripal_views	27dadbfc37 Removed requirement to have a 'comment' in the views integration import	před 12 roky
.gitignore	455df59fcc removing empty lines	před 13 roky
README.txt	a2d10bc7f7 Added describptive README and removed LISCENSE	před 12 roky

		
			
			
				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.

			
		