Mainlab Tripal Data Display

Mainlab Tripal Data Display contains a set of Drupal/PHP templates that organize and extend the default display of the biological data hosted on a Tripal-enabled site (i.e. http://tripal.info). Supported data type includes orgainsm, marker, QTL, germplasm (stock), map (featuremap), project, heritable phenotypic marker (MTL), environment (ND geolocation), haplotype block, polymorphism, eimage, generic gene (genes created by parsing Genbank files using the Mainlab 'tripal_genbank_parser' module), feature, and pub. Each of the templates can be turned on/off as desired. The module supports overriding built-in templates so site-specific customization is also supported (see Overriding templates under the Administration section). To take full advantage of these templates, data collecton templates and a loader (Mainlab Chado Loader, see https://github.com/tripal/mainlab_chado_loader/releases/latest) are also available as a separate module.

The Mainlab Tripal Data Display is created by Main Bioinformatics Lab (Main Lab) at Washington State University. Information about the Main Lab can be found at: https://www.bioinfo.wsu.edu

Requirement

• Drupal 7.x
• Tripal 7.x-2.x

Version

1.0.0

Download

The Mainlab Tripal Data Display module can be downloaded from GitHub:

https://www.github.com/tripal/mainlab_tripal/releases/latest

Installation

After downloading the module, extract it into your site's module directory (e.g. sites/all/modules) then follow the instructions below:

1. Enable the module either by

using the Drupal administrative interface: Go to: Modules, check Mainlab Tripal (under the Mainlab category) and save or using the 'drush' command:

drush pm-enable mainlab_tripal

2. Enable the templates as desired by visiting

   http://your.site/admin/mainlab/mainlab_tripal

Note: To get most out of these templates, please use the chado loader provided by the Main Lab to load data.

Administration

• Enabling/Disabling a template: Go to: Mainlab > Mainlab Tripal and check on the templates you want to enable i.e. http://your.site/admin/mainlab/mainlab_tripal

• Overriding templates

  1. Create a subfolder in the module directory 'mainlab_tripal/theme'. For example, 'mainlab_tripal/theme/custom_templates'

  2. Copy over any module-provided template (located in theme/template) or preprocessor (located in theme/preprocessors) you would like to modify to the folder you created and make changes accordingly.

  3. Go to the Mainlab Tripal administrative interface (i.e. http://your.site/admin/mainlab/mainlab_tripal) and enable overriding built-in templates by selecting the custom folder under the 'Override Default Templates' section. Save the configuration. Due to the Drupal's cache system, you will need to visit this page to save the configuration every time you copy over a new template. Otherwise the new template may not be used.

Showcase

This module is used by many web sites hosted at Main Bioinformatics Lab. You can visit [GDR] (http://www.rosaceae.org), [CottonGen] (http://www.cottongen.org), or [CSFL] (http://www.coolseasonfoodlegume.org) to see many of these templates in action. Please note that the templates will only show data that are available so they may look different from pages on your site.

• [Organism] (https://www.rosaceae.org/organism/Rubus/occidentalis)

• [Marker] (https://www.rosaceae.org/node/3898850)

• [Polymorphism] (https://www.rosaceae.org/polymorphism/3409955)

• [Allele] (https://www.rosaceae.org/allele/GD147/117/28)

• [QTL] (https://www.rosaceae.org/node/3883616)

• [MTL] (https://www.rosaceae.org/node/1532116)

• [Germplasm] (https://www.rosaceae.org/node/1794344)

• [Map] (https://www.rosaceae.org/node/1539087)

• [Project] (https://www.rosaceae.org/node/4230961)

Problems/Suggestions

Mainlab Tripal Data Display module is still under active development. For questions or bug report, please contact the developers at the Main Bioinformatics Lab by emailing to: dev@bioinfo.wsu.edu