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tripal
spficklin 9530be9e77 Chado installer is fully functional in Drupla 7 %!s(int64=11) %!d(string=hai) anos
docs b4086f5a04 Broke out API functions in the core into separate files %!s(int64=12) %!d(string=hai) anos
tripal_analysis fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader b4819f886d Fixed bug of exceeding max length when adding database description. Also, fixed error when loading file in bulk loader. Should have used a try,catch block %!s(int64=11) %!d(string=hai) anos
tripal_contact fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_core 9530be9e77 Chado installer is fully functional in Drupla 7 %!s(int64=11) %!d(string=hai) anos
tripal_cv fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_db fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_feature 9530be9e77 Chado installer is fully functional in Drupla 7 %!s(int64=11) %!d(string=hai) anos
tripal_featuremap fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_genetic fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_library fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity a59bff7fee Commented out ND default view %!s(int64=11) %!d(string=hai) anos
tripal_organism 55d6ec58ba Start converting tripal_core from 6.x to 7.x %!s(int64=11) %!d(string=hai) anos
tripal_phenotype fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_project fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_pub fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_stock fdd548a327 Removed old hook_views_data and hook_views_alter from all modules as the views integration now handles integrating all of the tables. Those were older functions used before views integration was completed. Also, fixed the joins of linker tables with nodes to be recipricol with base tables. If you used node as the base table you couldn't join on the corresponding chado table. That's fixed %!s(int64=11) %!d(string=hai) anos
tripal_views 5b5d1f92c5 Removed temp linking file for views %!s(int64=11) %!d(string=hai) anos
.gitignore 455df59fcc removing empty lines %!s(int64=13) %!d(string=hai) anos
README.txt 2c7002668c Tripal v1.0-fix1 %!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
--------------
1. Enable/Install the Tripal Core Module
2. Install a Chado database
- Either allow Tripal to add a chado database in a separate
schema to your Drupal database (recommended) by navigating to
Administer -> Tripal Management -> Install Chado
(admin/tripal/chado_1_11_install) and click "Install Chado" OR
- Edit the settings.php file to connect to an external chado
database
3. Enable/Install any other Tripal modules that are applicable to
your site.
4. Check the module page for each enabled Tripal module for further
module-specific instructions and a list of features and quick
links (Administer -> Tripal Managment -> [Module Name]


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 visualization of a 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.