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tripal
Stephen Ficklin d63f38a3e8 Merge branch '7.x-2.x' of git.drupal.org:sandbox/spficklin/1337878 into 7.x-2.x %!s(int64=11) %!d(string=hai) anos
docs 8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x %!s(int64=12) %!d(string=hai) anos
tripal_analysis c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader c1b87f555b Converted old API functions to new functions %!s(int64=11) %!d(string=hai) anos
tripal_contact c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_core c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_cv a3faf9f7ef Views: Created a function to handle making default views compatible with external chado instances by removing non-chado tables from the definition and implemented it for all chado default views. %!s(int64=11) %!d(string=hai) anos
tripal_db a3faf9f7ef Views: Created a function to handle making default views compatible with external chado instances by removing non-chado tables from the definition and implemented it for all chado default views. %!s(int64=11) %!d(string=hai) anos
tripal_example c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_feature c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_featuremap c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_genetic a3faf9f7ef Views: Created a function to handle making default views compatible with external chado instances by removing non-chado tables from the definition and implemented it for all chado default views. %!s(int64=11) %!d(string=hai) anos
tripal_library c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity a3faf9f7ef Views: Created a function to handle making default views compatible with external chado instances by removing non-chado tables from the definition and implemented it for all chado default views. %!s(int64=11) %!d(string=hai) anos
tripal_organism c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_phenotype a3faf9f7ef Views: Created a function to handle making default views compatible with external chado instances by removing non-chado tables from the definition and implemented it for all chado default views. %!s(int64=11) %!d(string=hai) anos
tripal_project c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_pub c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_stock c3d11a97cb updated chado_add_node_form_properties() to include better error checking and to use new chado_id and chado_id_field options %!s(int64=11) %!d(string=hai) anos
tripal_views ca9deb5988 Views :Added update integration function %!s(int64=11) %!d(string=hai) anos
.gitignore 455df59fcc removing empty lines %!s(int64=14) %!d(string=hai) anos
LICENSE.txt f8f44afa9c Added orphaned form items to sync form. Library module is now converted. %!s(int64=11) %!d(string=hai) anos
README.txt 8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x %!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
--------------
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.