zhxd2/tripal @ 09b02611ed98170720231fdd28fb285e36391331

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spficklin 09b02611ed Fixed memory leaks in the Tripal core API when storing the persistent connection. Alos fixed memory leaks in GFF loader and added loading of FASTA sequences embeded in the GFF file ##FASTA section		12 yıl önce
tripal_analysis	48631d702c Fixed a bug when registering a new analysis module. If the module already existed in the table it threw an error. Now it checks first. Also fixed bug with chado_query to not add a 'chado.' prefix in the 'substring' psql function. Also updated the tripal_core_chado_update module to return the primary key if a single record is updated and if the return_record option is given.	12 yıl önce
tripal_bulk_loader	9ea011d881 Added tripal_core_chado_clear_prepared function to clear previously prepared statements. Also changed chado. prefixing in chado query to only apply if there isn't already a prefix added.	12 yıl önce
tripal_contact	cd87d5a56a Fixed Drupal formatting standards	12 yıl önce
tripal_core	09b02611ed Fixed memory leaks in the Tripal core API when storing the persistent connection. Alos fixed memory leaks in GFF loader and added loading of FASTA sequences embeded in the GFF file ##FASTA section	12 yıl önce
tripal_cv	09b02611ed Fixed memory leaks in the Tripal core API when storing the persistent connection. Alos fixed memory leaks in GFF loader and added loading of FASTA sequences embeded in the GFF file ##FASTA section	12 yıl önce
tripal_db	42fe28540f Fixed issue #1712422. Changed all Chado querie to use chado_query() rather than db_query()	12 yıl önce
tripal_feature	09b02611ed Fixed memory leaks in the Tripal core API when storing the persistent connection. Alos fixed memory leaks in GFF loader and added loading of FASTA sequences embeded in the GFF file ##FASTA section	12 yıl önce
tripal_featuremap	9bb94c3748 Fixed issue #1699022. Took out all code that tried to distinguish a revision.	12 yıl önce
tripal_genetic	cd87d5a56a Fixed Drupal formatting standards	12 yıl önce
tripal_library	9bb94c3748 Fixed issue #1699022. Took out all code that tried to distinguish a revision.	12 yıl önce
tripal_natural_diversity	cd87d5a56a Fixed Drupal formatting standards	12 yıl önce
tripal_organism	9bb94c3748 Fixed issue #1699022. Took out all code that tried to distinguish a revision.	12 yıl önce
tripal_phenotype	cd87d5a56a Fixed Drupal formatting standards	12 yıl önce
tripal_project	9bb94c3748 Fixed issue #1699022. Took out all code that tried to distinguish a revision.	12 yıl önce
tripal_stock	9bb94c3748 Fixed issue #1699022. Took out all code that tried to distinguish a revision.	12 yıl önce
tripal_views	2ba111dac2 Oops should have put the code to add the chado schema to the SQL in a differnet place in the chado_query function.	12 yıl önce
.gitignore	455df59fcc removing empty lines	13 yıl önce
README.txt	a2d10bc7f7 Added describptive README and removed LISCENSE	12 yıl önce

		
			
			
				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.

			
		