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tripal
Stephen Ficklin ed72e47bcc 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 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader ed72e47bcc 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
tripal_contact 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_core 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_cv 2d134ac564 Fixed feature autocomplete %!s(int64=11) %!d(string=hai) anos
tripal_db 6bbb3eb45b Fixed access arguments for all menu items %!s(int64=11) %!d(string=hai) anos
tripal_example 34b866f276 Fixed merge conflict and changed 'Details' to 'Overview' on node pages %!s(int64=11) %!d(string=hai) anos
tripal_feature 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_featuremap 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_genetic 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_library 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_organism 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_phenotype 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_project 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_pub 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_stock 8c8af381a2 Updated class and id names of templates to be consistent %!s(int64=11) %!d(string=hai) anos
tripal_views ccb384e703 Replaced tabs with two spaces... updated node template %!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.