spficklin
2840b98e85
All node types (except stock) have a function to cleanup orphaned nodes but it wasn't complete for some. A new core API function was created that all modules with node types can use to clean up orphaned nodes. Also, the drush trpjob-run command was fixed so that a username must be provided to run the job
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%!s(int64=12) %!d(string=hai) anos | |
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| tripal_analysis | %!s(int64=12) %!d(string=hai) anos | |
| tripal_bulk_loader | %!s(int64=12) %!d(string=hai) anos | |
| tripal_contact | %!s(int64=12) %!d(string=hai) anos | |
| tripal_core | %!s(int64=12) %!d(string=hai) anos | |
| tripal_cv | %!s(int64=12) %!d(string=hai) anos | |
| tripal_db | %!s(int64=12) %!d(string=hai) anos | |
| tripal_feature | %!s(int64=12) %!d(string=hai) anos | |
| tripal_genetic | %!s(int64=12) %!d(string=hai) anos | |
| tripal_library | %!s(int64=12) %!d(string=hai) anos | |
| tripal_natural_diversity | %!s(int64=12) %!d(string=hai) anos | |
| tripal_organism | %!s(int64=12) %!d(string=hai) anos | |
| tripal_phenotype | %!s(int64=12) %!d(string=hai) anos | |
| tripal_project | %!s(int64=12) %!d(string=hai) anos | |
| tripal_stock | %!s(int64=12) %!d(string=hai) anos | |
| tripal_views | %!s(int64=12) %!d(string=hai) anos | |
| .gitignore | %!s(int64=13) %!d(string=hai) anos | |
| README.txt | %!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.
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.