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tripal
spficklin 148362fb34 Fixed bug in automatic citation generation 11 years ago
docs dd6d29004d Fixed size limit in pub importer text field. Updated doxygen config file 11 years ago
tripal_analysis 98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set 11 years ago
tripal_bulk_loader 98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set 11 years ago
tripal_contact 98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set 11 years ago
tripal_core 39e90c2263 Fixed bug resulting from accidental typo in the organism node_info hook that was introduced in the last push 11 years ago
tripal_cv a43ef3d007 Made feature node use autocomplete field for type when creating/editing a feature. Also added additional docuemntation for how to add property types to analysies and featuremaps when editing/inserting 11 years ago
tripal_db 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 11 years ago
tripal_feature 98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set 11 years ago
tripal_featuremap 98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set 11 years ago
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 11 years ago
tripal_library 98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set 11 years ago
tripal_natural_diversity a59bff7fee Commented out ND default view 11 years ago
tripal_organism 39e90c2263 Fixed bug resulting from accidental typo in the organism node_info hook that was introduced in the last push 11 years ago
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 11 years ago
tripal_project 98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set 11 years ago
tripal_pub 148362fb34 Fixed bug in automatic citation generation 11 years ago
tripal_stock 98edb56e8d Fixed bug in permissions for all modules that create node types. When testing if a node type should be created the function should always return true if the permission is set 11 years ago
tripal_views 7fcdb3edf6 Fixed incompatibility with PHP 5.4 11 years ago
.gitignore 455df59fcc removing empty lines 13 years ago
README.txt 9c0fdf6d45 Tripal release v1.1 - 2013/06/24 11 years ago

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.