zhxd2/tripal @ deb9d0059fc991b01891cba9c8543f3edbc74b37

Ei kuvausta

Stephen Ficklin deb9d0059f Improved admin delete feature interface, added API for analysis select options, updated GFF to add proteins if not in GFF, fixed a few bugs		10 vuotta sitten
docs	8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x	12 vuotta sitten
tripal_analysis	deb9d0059f Improved admin delete feature interface, added API for analysis select options, updated GFF to add proteins if not in GFF, fixed a few bugs	10 vuotta sitten
tripal_bulk_loader	6a812e5652 Switch #markup to #theme & #node in hook_node_view() to ensure that pages are not rendered ahead of time allowing modules to modify the panes being rendered	10 vuotta sitten
tripal_contact	846b344b19 Fixed memory leaks on syncing	10 vuotta sitten
tripal_core	deb9d0059f Improved admin delete feature interface, added API for analysis select options, updated GFF to add proteins if not in GFF, fixed a few bugs	10 vuotta sitten
tripal_cv	6230b71886 Changed package to 'tripal' for all modules	11 vuotta sitten
tripal_db	6230b71886 Changed package to 'tripal' for all modules	11 vuotta sitten
tripal_example	9cab666d85 Fixed error in example module	10 vuotta sitten
tripal_feature	deb9d0059f Improved admin delete feature interface, added API for analysis select options, updated GFF to add proteins if not in GFF, fixed a few bugs	10 vuotta sitten
tripal_featuremap	846b344b19 Fixed memory leaks on syncing	10 vuotta sitten
tripal_genetic	6f22290db5 Missed non-node hook_view_node implementations: now switched to #theme as well	10 vuotta sitten
tripal_library	846b344b19 Fixed memory leaks on syncing	10 vuotta sitten
tripal_natural_diversity	6f22290db5 Missed non-node hook_view_node implementations: now switched to #theme as well	10 vuotta sitten
tripal_organism	deb9d0059f Improved admin delete feature interface, added API for analysis select options, updated GFF to add proteins if not in GFF, fixed a few bugs	10 vuotta sitten
tripal_phenotype	6f22290db5 Missed non-node hook_view_node implementations: now switched to #theme as well	10 vuotta sitten
tripal_project	846b344b19 Fixed memory leaks on syncing	10 vuotta sitten
tripal_pub	ff2a43e41b Fixed memory leak in changing of URLs	10 vuotta sitten
tripal_stock	8bebb35274 Resolved merge conflict where we both fixed the same bug (in stock & feature check ->op is set before ensuring it's save on validation of node form)	10 vuotta sitten
tripal_views	faa9546d67 Views Integration (Issue #2479599): Additional Ramifications since the unset mview_id was used to detect legacy mviews repeatedly, there needed to be fixes in the hook_views_data() and views integration UI	10 vuotta sitten
README.txt	8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x	12 vuotta sitten

		
			
			
				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
--------------
Please follow the online tutorial for installation instructions:
http://www.gmod.org/wiki/Tripal_Tutorial_v1.1


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 a large 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. 

			
		