zhxd2/tripal @ 5888809fd2118fc1d87e4fde4d2aea0ccec1e9ef

Sen descrición

1947 Achegas

Lacey Sanderson 5888809fd2 Bulk Loader: Moved node functionality into a chado_node.inc file and moved a preprocess hook into the theme.inc file		%!s(int64=11) %!d(string=hai) anos
docs	8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x	%!s(int64=11) %!d(string=hai) anos
tripal_analysis	3433d53fd8 All pub templates converted (but some need testing), made all sync functions for all modules consistent and added a session variable for getting pager counts	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	5888809fd2 Bulk Loader: Moved node functionality into a chado_node.inc file and moved a preprocess hook into the theme.inc file	%!s(int64=11) %!d(string=hai) anos
tripal_contact	3433d53fd8 All pub templates converted (but some need testing), made all sync functions for all modules consistent and added a session variable for getting pager counts	%!s(int64=11) %!d(string=hai) anos
tripal_core	eddf24c3c6 Updated some code comments	%!s(int64=11) %!d(string=hai) anos
tripal_cv	97cdd4c4d1 pub module can now insert/update/delete pubs. Base templates, pub type templates and teaser is working	%!s(int64=11) %!d(string=hai) anos
tripal_db	5f710e226b Changed Chado API to use array for indicating status of Chado as it was slowing down loaders the previous way	%!s(int64=11) %!d(string=hai) anos
tripal_feature	3433d53fd8 All pub templates converted (but some need testing), made all sync functions for all modules consistent and added a session variable for getting pager counts	%!s(int64=11) %!d(string=hai) anos
tripal_featuremap	30aa5f6cad Nightly checkin... working on pub module. Fixed bugs in other modules and consistency issues	%!s(int64=11) %!d(string=hai) anos
tripal_genetic	14c01a96cd Genotypes: Added entire admin menu including default admin view	%!s(int64=11) %!d(string=hai) anos
tripal_library	30aa5f6cad Nightly checkin... working on pub module. Fixed bugs in other modules and consistency issues	%!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity	8335722371 Merge branch '7.x-2.x' of git.drupal.org:sandbox/spficklin/1337878 into 7.x-2.x	%!s(int64=11) %!d(string=hai) anos
tripal_organism	b5bebdc890 Nightly checkin	%!s(int64=11) %!d(string=hai) anos
tripal_phenotype	f1745a985b Fixed bug in views integration to allow more than one join to the same table & fixed phenotype admin view	%!s(int64=11) %!d(string=hai) anos
tripal_project	30aa5f6cad Nightly checkin... working on pub module. Fixed bugs in other modules and consistency issues	%!s(int64=11) %!d(string=hai) anos
tripal_pub	53dbe7f977 Pub importers on the command-line are working for both PubMed and AGL	%!s(int64=11) %!d(string=hai) anos
tripal_stock	e03dbdeb59 Stock: Implemented the properties api in stock nodes	%!s(int64=11) %!d(string=hai) anos
tripal_views	ee855ade6e All templates for the feature page are converted except featurepos and phenotype needs testing.	%!s(int64=11) %!d(string=hai) anos
.gitignore	455df59fcc removing empty lines	%!s(int64=13) %!d(string=hai) anos
README.txt	8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x	%!s(int64=11) %!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
--------------
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. 

			
		