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tripal
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Ficklin f3f17b6ec1 Fixed merge conflict %!s(int64=9) %!d(string=hai) anos
docs dd6d29004d Fixed size limit in pub importer text field. Updated doxygen config file %!s(int64=11) %!d(string=hai) anos
tripal_analysis 1b513eb0fb Small bug fixes %!s(int64=10) %!d(string=hai) anos
tripal_bulk_loader 24cf39f91b added template for the organism references, anf fixed obo loader when missing default namespace %!s(int64=10) %!d(string=hai) anos
tripal_contact 3388ff58d8 Various bug fixes discovered in the process of converting to Drupal 7 %!s(int64=10) %!d(string=hai) anos
tripal_core 2fa23ec5b4 bug fixes for strict PHP %!s(int64=11) %!d(string=hai) anos
tripal_cv 24cf39f91b added template for the organism references, anf fixed obo loader when missing default namespace %!s(int64=10) %!d(string=hai) anos
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 %!s(int64=11) %!d(string=hai) anos
tripal_feature f3f17b6ec1 Fixed merge conflict %!s(int64=9) %!d(string=hai) anos
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 %!s(int64=11) %!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=11) %!d(string=hai) anos
tripal_library ff37627b86 Added ability to set URLs for stocks. Added ability to configure format of stock and feature page titles. Changed the stock syncing to match that of features. Removed the ability to set the title for stocks and features. Titles get set automatically now. %!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity 0c408f3863 Added chado eimage node type (in a new Tripal Eimage module) and chado nd_geolocation node type (in Tripal Natural Diversity module) %!s(int64=10) %!d(string=hai) anos
tripal_organism 24cf39f91b added template for the organism references, anf fixed obo loader when missing default namespace %!s(int64=10) %!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=11) %!d(string=hai) anos
tripal_project 87e6c5f4bf Removed the listing of all images for the sync admin interface. %!s(int64=10) %!d(string=hai) anos
tripal_pub 36bd0104f8 Fix for AGL importer %!s(int64=10) %!d(string=hai) anos
tripal_stock 20731f50b9 Added check for length of URL exceeding 128 chars %!s(int64=11) %!d(string=hai) anos
tripal_views 3388ff58d8 Various bug fixes discovered in the process of converting to Drupal 7 %!s(int64=10) %!d(string=hai) anos
.gitignore 455df59fcc removing empty lines %!s(int64=13) %!d(string=hai) anos
LICENSE.txt 3388ff58d8 Various bug fixes discovered in the process of converting to Drupal 7 %!s(int64=10) %!d(string=hai) anos
README.txt 9c0fdf6d45 Tripal release v1.1 - 2013/06/24 %!s(int64=11) %!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
--------------
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.