zhxd2/tripal @ 9d7bf94295a7d61751728b555a705432feea710e

Sen descrición

spficklin 9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism		%!s(int64=12) %!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	9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism	%!s(int64=12) %!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=12) %!d(string=hai) anos
tripal_contact	9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism	%!s(int64=12) %!d(string=hai) anos
tripal_core	9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism	%!s(int64=12) %!d(string=hai) anos
tripal_cv	b3b5061ff7 admin functions of Tripal cv module are working with drupal 7.	%!s(int64=12) %!d(string=hai) anos
tripal_db	b3b5061ff7 admin functions of Tripal cv module are working with drupal 7.	%!s(int64=12) %!d(string=hai) anos
tripal_feature	9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism	%!s(int64=12) %!d(string=hai) anos
tripal_featuremap	9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism	%!s(int64=12) %!d(string=hai) anos
tripal_genetic	fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed	%!s(int64=12) %!d(string=hai) anos
tripal_library	9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism	%!s(int64=12) %!d(string=hai) anos
tripal_natural_diversity	a59bff7fee Commented out ND default view	%!s(int64=12) %!d(string=hai) anos
tripal_organism	9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism	%!s(int64=12) %!d(string=hai) anos
tripal_phenotype	fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed	%!s(int64=12) %!d(string=hai) anos
tripal_project	9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism	%!s(int64=12) %!d(string=hai) anos
tripal_pub	9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism	%!s(int64=12) %!d(string=hai) anos
tripal_stock	9d7bf94295 Changed chado_get_id_for_node API call to accept nid as second parameter and fixed all calls in all modules. Organism module can now sync, edit, upload image for an organism	%!s(int64=12) %!d(string=hai) anos
tripal_views	5b5d1f92c5 Removed temp linking file for views	%!s(int64=12) %!d(string=hai) anos
.gitignore	455df59fcc removing empty lines	%!s(int64=14) %!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. 

			
		