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tripal
Stephen Ficklin 80b9efb84e Added API functions for inserting Bulk loaders. Also fixed bulk loader so it imports and exports JSON format strings. It also is backwards compatible (needs to be removed eventually) for loading serialized PHP and stringified PHP arrays. The Tripal Extensions Import admin page only supports import of JSON strings for security purposes %!s(int64=10) %!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 deb9d0059f Improved admin delete feature interface, added API for analysis select options, updated GFF to add proteins if not in GFF, fixed a few bugs %!s(int64=10) %!d(string=hai) anos
tripal_bulk_loader 80b9efb84e Added API functions for inserting Bulk loaders. Also fixed bulk loader so it imports and exports JSON format strings. It also is backwards compatible (needs to be removed eventually) for loading serialized PHP and stringified PHP arrays. The Tripal Extensions Import admin page only supports import of JSON strings for security purposes %!s(int64=10) %!d(string=hai) anos
tripal_contact 846b344b19 Fixed memory leaks on syncing %!s(int64=10) %!d(string=hai) anos
tripal_core 80b9efb84e Added API functions for inserting Bulk loaders. Also fixed bulk loader so it imports and exports JSON format strings. It also is backwards compatible (needs to be removed eventually) for loading serialized PHP and stringified PHP arrays. The Tripal Extensions Import admin page only supports import of JSON strings for security purposes %!s(int64=10) %!d(string=hai) anos
tripal_cv 6230b71886 Changed package to 'tripal' for all modules %!s(int64=10) %!d(string=hai) anos
tripal_db 6230b71886 Changed package to 'tripal' for all modules %!s(int64=10) %!d(string=hai) anos
tripal_example 9cab666d85 Fixed error in example module %!s(int64=10) %!d(string=hai) anos
tripal_feature 80b9efb84e Added API functions for inserting Bulk loaders. Also fixed bulk loader so it imports and exports JSON format strings. It also is backwards compatible (needs to be removed eventually) for loading serialized PHP and stringified PHP arrays. The Tripal Extensions Import admin page only supports import of JSON strings for security purposes %!s(int64=10) %!d(string=hai) anos
tripal_featuremap 846b344b19 Fixed memory leaks on syncing %!s(int64=10) %!d(string=hai) anos
tripal_genetic 6f22290db5 Missed non-node hook_view_node implementations: now switched to #theme as well %!s(int64=10) %!d(string=hai) anos
tripal_library 846b344b19 Fixed memory leaks on syncing %!s(int64=10) %!d(string=hai) anos
tripal_natural_diversity 6f22290db5 Missed non-node hook_view_node implementations: now switched to #theme as well %!s(int64=10) %!d(string=hai) anos
tripal_organism deb9d0059f Improved admin delete feature interface, added API for analysis select options, updated GFF to add proteins if not in GFF, fixed a few bugs %!s(int64=10) %!d(string=hai) anos
tripal_phenotype 6f22290db5 Missed non-node hook_view_node implementations: now switched to #theme as well %!s(int64=10) %!d(string=hai) anos
tripal_project 846b344b19 Fixed memory leaks on syncing %!s(int64=10) %!d(string=hai) anos
tripal_pub ff2a43e41b Fixed memory leak in changing of URLs %!s(int64=10) %!d(string=hai) anos
tripal_stock c324fbd404 Bug Fix: Stock module didn't check organism/type_id was set before using it to check uniquename uniqueness. %!s(int64=10) %!d(string=hai) anos
tripal_views faa9546d67 Views Integration (Issue #2479599): Additional Ramifications since the unset mview_id was used to detect legacy mviews repeatedly, there needed to be fixes in the hook_views_data() and views integration UI %!s(int64=10) %!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.