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tripal
Lacey Sanderson 346189b453 Chado Node API: Bug Fixes 1) Subject & Object were reversed in display; 2) use a unique id instead of rank to ensure all relationships are displayed (rank doesn't work b/c Fred is_paternal_parent_of Max and Max is_paternal_parent_of Lui might have the same rank) %!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 4464f631c6 Updated default user search views to have access permission & fixed some permissions bugs in the process %!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader 2d50dc229e Bulk Loader: fixed field adding error and added checking for FALSE template/record/field_id in path %!s(int64=11) %!d(string=hai) anos
tripal_contact 4464f631c6 Updated default user search views to have access permission & fixed some permissions bugs in the process %!s(int64=11) %!d(string=hai) anos
tripal_core 346189b453 Chado Node API: Bug Fixes 1) Subject & Object were reversed in display; 2) use a unique id instead of rank to ensure all relationships are displayed (rank doesn't work b/c Fred is_paternal_parent_of Max and Max is_paternal_parent_of Lui might have the same rank) %!s(int64=11) %!d(string=hai) anos
tripal_cv d33cf2fcde CV Defaults: Added the ability to add in new cv defaults through the web UI %!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 4464f631c6 Updated default user search views to have access permission & fixed some permissions bugs in the process %!s(int64=11) %!d(string=hai) anos
tripal_featuremap 4464f631c6 Updated default user search views to have access permission & fixed some permissions bugs in the process %!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 4464f631c6 Updated default user search views to have access permission & fixed some permissions bugs in the process %!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 4464f631c6 Updated default user search views to have access permission & fixed some permissions bugs in the process %!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 4464f631c6 Updated default user search views to have access permission & fixed some permissions bugs in the process %!s(int64=11) %!d(string=hai) anos
tripal_pub 2c6657d84c Added update functions for custom tables where fK relationships were missing. Fixed other bugs and removed ability to edit legacy MViews %!s(int64=11) %!d(string=hai) anos
tripal_stock 87dd5df1fd Stock: Updated load to use a preset stock_id rather then always using chado_get_id_from_nid %!s(int64=11) %!d(string=hai) anos
tripal_views fa1525e439 Views: Added a generic select list by ID filter handler which works on any foreign key as long as the referenced table has a name field %!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.