zhxd2/tripal @ cdade360dfd53982fff0a4704d47fbe796b6a1e5

Sen descrición

Lacey Sanderson cdade360df Added checkbox allowing user to enable/disable keeping track of inserted record IDs on a per bulk loading job basis. The default for already existing bulk loader jobs is TRUE and the default for new bulk loader jobs is FALSE		%!s(int64=12) %!d(string=hai) anos
extensions	df72dd3821 Moved Tripal GBrowse out to it's own git repository	%!s(int64=12) %!d(string=hai) anos
tripal_analysis	14835a0ec9 Added additional documentation to tripal_analysis function headers	%!s(int64=12) %!d(string=hai) anos
tripal_bulk_loader	cdade360df Added checkbox allowing user to enable/disable keeping track of inserted record IDs on a per bulk loading job basis. The default for already existing bulk loader jobs is TRUE and the default for new bulk loader jobs is FALSE	%!s(int64=12) %!d(string=hai) anos
tripal_contact	26a385d35d Tripal Contact adheres to Drupal coding standards	%!s(int64=12) %!d(string=hai) anos
tripal_core	9001868cf7 Fixed a bug in the chado_expand_vars API function call. When a foreign key relationship existed with the same table twice (e.g. subject_id and object_id both map to feature_id in the feature_relationship table) then only one of the relationships would appear in the resulting object	%!s(int64=12) %!d(string=hai) anos
tripal_cv	18d7fa4d75 Updated 6.x-1482618-API_for_default_views_integration branch to current 6.x-0.4-dev	%!s(int64=12) %!d(string=hai) anos
tripal_db	9eb5665af7 Coding Standards: Final cleanup for tripal_db; added @coder-ignore for errors to be ignored	%!s(int64=12) %!d(string=hai) anos
tripal_feature	cfff5f8594 Merge branch '6.x-0.4-dev' of git.drupal.org:sandbox/spficklin/1337878 into 6.x-0.4-dev	%!s(int64=12) %!d(string=hai) anos
tripal_genetic	d695934531 Merge branch '6.x-0.4-dev' into 6.x-1617096-unify_coding_style	%!s(int64=12) %!d(string=hai) anos
tripal_library	2640a022a1 Tripal Library adheres to Drupal coding standads	%!s(int64=12) %!d(string=hai) anos
tripal_natural_diversity	fda25886b5 Tripal Natural Diversity adhere to Drupal coding standards	%!s(int64=12) %!d(string=hai) anos
tripal_organism	aaed62d7f5 Tripal Organism adheres to Drupal coding standards	%!s(int64=12) %!d(string=hai) anos
tripal_phenotype	4c052af735 Tripal Phenotype adheres to Drupal coding standards	%!s(int64=12) %!d(string=hai) anos
tripal_project	d9569ba525 Tripal Project adheres to Drupal coding standards	%!s(int64=12) %!d(string=hai) anos
tripal_pub	3dd051aecb Coding Standards: Final cleanup for tripal_pub; added @coder-ignore for errors to be ignored	%!s(int64=12) %!d(string=hai) anos
tripal_search	73c9af1773 Coding Standards: Final cleanup for tripal_search; added @coder-ignore for errors to be ignored	%!s(int64=12) %!d(string=hai) anos
tripal_stock	6d99d6473d Coding Standards: Final cleanup for tripal_stock; added @coder-ignore for errors to be ignored	%!s(int64=12) %!d(string=hai) anos
tripal_views	18d7fa4d75 Updated 6.x-1482618-API_for_default_views_integration branch to current 6.x-0.4-dev	%!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.

			
		