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tripal
Stephen Ficklin 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!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=11) %!d(string=hai) anos
tripal_analysis 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!s(int64=11) %!d(string=hai) anos
tripal_api e8c22d49b5 Created a new Tripal API module containing the chado node properties api and function wrappers for the old properties api %!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader 49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module %!s(int64=11) %!d(string=hai) anos
tripal_contact 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!s(int64=11) %!d(string=hai) anos
tripal_core 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!s(int64=11) %!d(string=hai) anos
tripal_cv 49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module %!s(int64=11) %!d(string=hai) anos
tripal_db 49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module %!s(int64=11) %!d(string=hai) anos
tripal_example 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!s(int64=11) %!d(string=hai) anos
tripal_feature 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!s(int64=11) %!d(string=hai) anos
tripal_featuremap 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!s(int64=11) %!d(string=hai) anos
tripal_genetic 4b664d7114 ND module done... will need more testing with large dataset %!s(int64=11) %!d(string=hai) anos
tripal_library 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity 2cedc4943b Fixed bug in stock module that made genotypes show up twice %!s(int64=11) %!d(string=hai) anos
tripal_organism 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!s(int64=11) %!d(string=hai) anos
tripal_phenotype 8bd0b15d71 Fixed phenotype module to include the tripal_feature.phenotype.tpl.php template %!s(int64=11) %!d(string=hai) anos
tripal_project 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!s(int64=11) %!d(string=hai) anos
tripal_pub 0bd1f019a7 Updated modules with nodes to use new sync functionality. Working on supporting checkboxes in syncing as well... not quite done %!s(int64=11) %!d(string=hai) anos
tripal_stock df26ed8bea Stock templates converted. Fixed some other templates %!s(int64=11) %!d(string=hai) anos
tripal_views 49527af90a Fixed type in .install file for all modules. Updated tripal_genetic templates. Working on ND module %!s(int64=11) %!d(string=hai) anos
.gitignore 455df59fcc removing empty lines %!s(int64=13) %!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=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.