zhxd2/tripal @ a53f6c44a2ad023bb88102c71ed9f8b0c67bb331

Sen descrición

spficklin a53f6c44a2 Fixing bug in sequence retrieval function in feature API		%!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	7e1b88f37e Updated version to 6.x-1.1 in anticipation of upcoming release. Fixed bug in Features view so that the name field appears.	%!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader	b4819f886d Fixed bug of exceeding max length when adding database description. Also, fixed error when loading file in bulk loader. Should have used a try,catch block	%!s(int64=11) %!d(string=hai) anos
tripal_contact	4c8824efcd Added contact configuration page and admin theme page. Also added template for contact publications	%!s(int64=11) %!d(string=hai) anos
tripal_core	7e1b88f37e Updated version to 6.x-1.1 in anticipation of upcoming release. Fixed bug in Features view so that the name field appears.	%!s(int64=11) %!d(string=hai) anos
tripal_cv	7e1b88f37e Updated version to 6.x-1.1 in anticipation of upcoming release. Fixed bug in Features view so that the name field appears.	%!s(int64=11) %!d(string=hai) anos
tripal_db	18ea428353 Added ability to add properties and DBxref's to featuremaps. Added featuremapprop and featuremap_dbxref tables to the featuremap installer	%!s(int64=11) %!d(string=hai) anos
tripal_feature	a53f6c44a2 Fixing bug in sequence retrieval function in feature API	%!s(int64=11) %!d(string=hai) anos
tripal_featuremap	4c8824efcd Added contact configuration page and admin theme page. Also added template for contact publications	%!s(int64=11) %!d(string=hai) anos
tripal_genetic	9bc1a12eac Moved the stock_genotype theme to the genetic module. Technically it is part of the stock module, but the tables behave similarly to the feature_genotype table and are both superceeded by the nd tables. Since it the themes fit better with the genetic module they have been moved there	%!s(int64=11) %!d(string=hai) anos
tripal_library	7e1b88f37e Updated version to 6.x-1.1 in anticipation of upcoming release. Fixed bug in Features view so that the name field appears.	%!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity	8a6b0f5dfc Fixed the stock_nd_genotype template and removed the stock_gelocation template	%!s(int64=11) %!d(string=hai) anos
tripal_organism	7e1b88f37e Updated version to 6.x-1.1 in anticipation of upcoming release. Fixed bug in Features view so that the name field appears.	%!s(int64=11) %!d(string=hai) anos
tripal_phenotype	7e1b88f37e Updated version to 6.x-1.1 in anticipation of upcoming release. Fixed bug in Features view so that the name field appears.	%!s(int64=11) %!d(string=hai) anos
tripal_project	fdac2a25b5 Type in permission	%!s(int64=11) %!d(string=hai) anos
tripal_pub	18ea428353 Added ability to add properties and DBxref's to featuremaps. Added featuremapprop and featuremap_dbxref tables to the featuremap installer	%!s(int64=11) %!d(string=hai) anos
tripal_stock	9bc1a12eac Moved the stock_genotype theme to the genetic module. Technically it is part of the stock module, but the tables behave similarly to the feature_genotype table and are both superceeded by the nd tables. Since it the themes fit better with the genetic module they have been moved there	%!s(int64=11) %!d(string=hai) anos
tripal_views	7e1b88f37e Updated version to 6.x-1.1 in anticipation of upcoming release. Fixed bug in Features view so that the name field appears.	%!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. 

			
		