zhxd2/tripal @ 0d959b839401bc31acab75662956bdb919f32194

Sen descrición

Stephen Ficklin 0d959b8394 Fixed bug with searching by publication type. It was only looking in properties		%!s(int64=11) %!d(string=hai) anos
docs	b4086f5a04 Broke out API functions in the core into separate files	%!s(int64=12) %!d(string=hai) anos
tripal_analysis	ef7557839c Forgot file	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	b8257936dc Fixed bug when adding a custom table that already exists. It wouldn't let it happen despite that the code was smart enough to handle it correctly.	%!s(int64=12) %!d(string=hai) anos
tripal_contact	84bb403b7d Added new term to pub ontology. and moved location of contact ontology	%!s(int64=11) %!d(string=hai) anos
tripal_core	079f9f0375 Moved form elements from views module to Tripal core and updated seq extract form to use the file upload combo element. Also renamed include files to have a .inc extension rather than a .php extension in the core moduel	%!s(int64=11) %!d(string=hai) anos
tripal_cv	dacb3542df Added several configurable options for allow end-user to specify how to find duplicate publications	%!s(int64=11) %!d(string=hai) anos
tripal_db	aa118aca79 Fixed bugs, changed the way authors lists are stored, updated ontology	%!s(int64=12) %!d(string=hai) anos
tripal_feature	e557f16da4 Added specific handling of Patent type publications. Fixed the tpub.obo as some of the accessions were missing the colon between the DB name and number.	%!s(int64=11) %!d(string=hai) anos
tripal_featuremap	177c6c053b Decided to backtrack version to 1.0-fix1 rather than 1.1. Will tag a small bug fix release for the Tripal tutorial	%!s(int64=12) %!d(string=hai) anos
tripal_genetic	177c6c053b Decided to backtrack version to 1.0-fix1 rather than 1.1. Will tag a small bug fix release for the Tripal tutorial	%!s(int64=12) %!d(string=hai) anos
tripal_library	1400425db6 Added configuration page to tripal_pub module	%!s(int64=12) %!d(string=hai) anos
tripal_natural_diversity	177c6c053b Decided to backtrack version to 1.0-fix1 rather than 1.1. Will tag a small bug fix release for the Tripal tutorial	%!s(int64=12) %!d(string=hai) anos
tripal_organism	4622aa3c46 Fixed bug with syncing organisms	%!s(int64=12) %!d(string=hai) anos
tripal_phenotype	177c6c053b Decided to backtrack version to 1.0-fix1 rather than 1.1. Will tag a small bug fix release for the Tripal tutorial	%!s(int64=12) %!d(string=hai) anos
tripal_project	b405ae3afb Continued development of Contact and Publiation modules	%!s(int64=12) %!d(string=hai) anos
tripal_pub	0d959b8394 Fixed bug with searching by publication type. It was only looking in properties	%!s(int64=11) %!d(string=hai) anos
tripal_stock	2756a7cce1 Added brackets around all table names in SQL statements throughout all of Tripal	%!s(int64=12) %!d(string=hai) anos
tripal_views	079f9f0375 Moved form elements from views module to Tripal core and updated seq extract form to use the file upload combo element. Also renamed include files to have a .inc extension rather than a .php extension in the core moduel	%!s(int64=11) %!d(string=hai) anos
.gitignore	455df59fcc removing empty lines	%!s(int64=13) %!d(string=hai) anos
README.txt	2c7002668c Tripal v1.0-fix1	%!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. 

			
		