Tripal Extensions

The following is a list of extensions that have been provided by Tripal site developers and which can be imported into another Tripal site. If you have custom extensions you would like to share, please let us know by joining the Tripal mailing list and sending a request. Consider adding your extensions even if only in development state as this encourages collaboration and reduces duplication of effort. Use the fields below to filter.
Extension Module
Provides a content type for downloadable files. Individual downloads can optionally be exposed as JBrowse tracks through Tripal JBrowse API.
Extension Module
Implementation of the popular search engine Elasticsearch for the chado database tables. Provides an administrative interface for Elasticsearch Index management and cross-site search setup. Tripal 3 support includes an organism specific gene search field and collections integration.
Extension Module
The Tripal Fields Generator is a CLI tool for developers. While not a module per se, Fields Generator greatly simplifies the process of defining fields programmaticaly by collection information on the cvterm for the field and automatically generating the field.inc, field_formatter.inc, and field_widget.inc files. Can connect to your database and verify your cvterm information to prevent accidental insertion of erroneous terms.
Extension Module
This module extends Tripal to support association of files with data stored in the Chado database. The module will also provide an API to allow other modules to create "plugins" for specific file types. The module is still in development but it is expected that it will provide plugins for Images, BAM and VCF files. These plugins will provide the functionality for visualization and access to these types of files. This file is of importance to the future Tripal Exchange module will provide web services for data house in Chado and in files.<p>
Extension Module
This module extends the Tripal Analysis Module that comes with Tripal, and provides loaders and viewers for InterProScan v4 and v5 results. It does not provide a service for performing InterProScan analyses. This module imports results in XML format. Features that are loaded into Chado will automatically have InterProScan results associated and results will be visible on the feature's page.
Extension Module
This module exposes Chado as a JBrowse-compatible REST API.
Extension Module
This module extends the Tripal Analysis Module that comes with Tripal, and provides loaders and viewers for results generated using the KEGG/KAAS tool at http://www.genome.jp/tools/kaas/. It does not provide a service for performing KEGG analyses. This module imports results in the KEGG hier format. Features that are loaded into Chado will automatically have KEGG Orthologs and Pathways associated and results will be visible on the feature's page. A KEGG report is also made available on the KEGG analysis page allowing the user to browse all the results from the entire analysis. Note: KEGG has recently stopped offering the heir file format from it's service. Therefore this module is currently only useful for older files.
Extension Module
Supports multiple Chado instances in one Tripal installation. Chado instances must be in the same database in different schemata. By default, Chado instance selection is made on a user basis: the administrator can enter in the system the connection information for several Chado databases and assign to each user a specific Chado connection setting. However, a companion module, included with this module, allows users to select which instance of Chado they want to use through a Drupal block dropdown menu. Note: it's also possible to only use one Chado instance with different user accounts to access to that database. Why multiple Chado instances? There are many reasons and just to give a few: private/public sites, dev/staging/prod, multiple organisms, multiple versions of genomes,... With the multi-chado module, all thoses instances can share a same common Drupal site (configured and with the same users of course).
Extension Module
Supports management of network data, in particular for gene co-expression data. This module is in use on the GenNetEngine. It is still currently being revamped for general use.
Extension Module
This module provides d3.js integration for Tripal with the intent of providing common biological diagrams such as: Pie &amp; Bar charts (Coming Soon), Sequence Coordinate Diagrams (ex: BLAST Hit diagram; Coming Soon), Pedigree Diagrams