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tripal
Nathan Weeks 2c224cc6da Issue #2463211: Updated the cvterm views handler to use loose index scan to generate the drop-down list %!s(int64=9) %!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 0d02183154 Merge branch '7.x-2.x' of git.drupal.org:project/tripal into 7.x-2.x %!s(int64=9) %!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=9) %!d(string=hai) anos
tripal_contact baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!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=9) %!d(string=hai) anos
tripal_cv baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!d(string=hai) anos
tripal_db baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!d(string=hai) anos
tripal_example 9cab666d85 Fixed error in example module %!s(int64=9) %!d(string=hai) anos
tripal_feature 0d02183154 Merge branch '7.x-2.x' of git.drupal.org:project/tripal into 7.x-2.x %!s(int64=9) %!d(string=hai) anos
tripal_featuremap baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!d(string=hai) anos
tripal_genetic baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!d(string=hai) anos
tripal_library baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!d(string=hai) anos
tripal_natural_diversity baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!d(string=hai) anos
tripal_organism 0d02183154 Merge branch '7.x-2.x' of git.drupal.org:project/tripal into 7.x-2.x %!s(int64=9) %!d(string=hai) anos
tripal_phenotype baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!d(string=hai) anos
tripal_project baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!d(string=hai) anos
tripal_pub baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!d(string=hai) anos
tripal_stock baac0be178 Issue #2463211: Set all administrative views to require input. This ensures that the page won't WSOD if there are too many records in the particular table. NOTE: this was a problem due to speed bottlenecks such as the drop-down filters and sorting of the results. %!s(int64=9) %!d(string=hai) anos
tripal_views 2c224cc6da Issue #2463211: Updated the cvterm views handler to use loose index scan to generate the drop-down list %!s(int64=9) %!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.