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tripal
Lacey Sanderson 02f5fa9c32 Bulk Loader: collapsed trasform field by default (unless regex are set) %!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 35ad015c6b Default Views: made them link to their content (both admin and search) using an accessory nid field re-written to form the URL %!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader 02f5fa9c32 Bulk Loader: collapsed trasform field by default (unless regex are set) %!s(int64=11) %!d(string=hai) anos
tripal_contact 35ad015c6b Default Views: made them link to their content (both admin and search) using an accessory nid field re-written to form the URL %!s(int64=11) %!d(string=hai) anos
tripal_core 3b15f3b503 Nightly checkin .... fixed some issues that caused log entries. working on adding CDS sequences to sequence page %!s(int64=11) %!d(string=hai) anos
tripal_cv ddf18ece9e Added missing files to example module. Working on default CV form %!s(int64=11) %!d(string=hai) anos
tripal_db 3b15f3b503 Nightly checkin .... fixed some issues that caused log entries. working on adding CDS sequences to sequence page %!s(int64=11) %!d(string=hai) anos
tripal_example ddf18ece9e Added missing files to example module. Working on default CV form %!s(int64=11) %!d(string=hai) anos
tripal_feature 35ad015c6b Default Views: made them link to their content (both admin and search) using an accessory nid field re-written to form the URL %!s(int64=11) %!d(string=hai) anos
tripal_featuremap 35ad015c6b Default Views: made them link to their content (both admin and search) using an accessory nid field re-written to form the URL %!s(int64=11) %!d(string=hai) anos
tripal_genetic 3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions %!s(int64=11) %!d(string=hai) anos
tripal_library 35ad015c6b Default Views: made them link to their content (both admin and search) using an accessory nid field re-written to form the URL %!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity 3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions %!s(int64=11) %!d(string=hai) anos
tripal_organism 35ad015c6b Default Views: made them link to their content (both admin and search) using an accessory nid field re-written to form the URL %!s(int64=11) %!d(string=hai) anos
tripal_phenotype 3147fcb63a Converted all tripal_generate_chado_var and tripal_expand_chado_vars to new API functions %!s(int64=11) %!d(string=hai) anos
tripal_project 35ad015c6b Default Views: made them link to their content (both admin and search) using an accessory nid field re-written to form the URL %!s(int64=11) %!d(string=hai) anos
tripal_pub 35ad015c6b Default Views: made them link to their content (both admin and search) using an accessory nid field re-written to form the URL %!s(int64=11) %!d(string=hai) anos
tripal_stock 35ad015c6b Default Views: made them link to their content (both admin and search) using an accessory nid field re-written to form the URL %!s(int64=11) %!d(string=hai) anos
tripal_views d315cb9035 Changed version number to match Drupal release tag conventions %!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.