Tripal Crop Configure

Provides drush commands to configure Tripal sites focused on crop and breeding research.

Drush Commands

enable-tcrop-modules (tcrop-enable)

Enables all the modules in the Tripal Crop package.

drush tcrop-enable

reset-tcrop-config (tcrop-config)

Resets the configuration for all Tripal Crop modules to the defaults.

drush tcrop-config

add-tcrop-species (tcrop-species)

Adds the specified species and configures the resource for it.

Arguements (required):

• genus
• species
• common_name
• abbreviation

drush tcrop-species Lens culinaris Lentil "L. culinaris"

reset-tcrop-display (tcrop-display)

Resets the display for all Tripal Content Types.

drush tcrop-display

Pre-requisites

• Drupal 7.x

• Tripal 3.x (including Tripal DS)

• the following Drupal and Tripal extension modules:

    chado_custom_search, trpfancy_fields, tripald3, trpdownload_api,
    analyzedphenotypes, divseek_search, nd_genotypes, tripal_elasticsearch,
    tripal_galaxy, tripal_jbrowse_page, tripal_jbrowse_mgmt,
    tripal_qtl, vcf_filter, tripal_germplasm_importer, tripal_map
  

It is recommended to use this module with Tripal Crop Docker which already contains all the above modules!

Future Work

• More automatic display configuration for even more intuitive pages for breeders.
• Automatic configuration of permissions.
• Integration with JBrowse and Galaxy.
• Automatic data submission to multiple modules (e.g. an VCF file could be added to VCF Filter, Tripal JBrowse, Tripal Galaxy and ND Genotypes)

Funding

The first iteration of the platform is funded under a Genome Canada Project with co-funding from other partners.

Citation

Lacey-Anne Sanderson, Kirstin E. Bett, Loren H. Rieseberg (2020) Tripal Crop Config: drush commands to configure Tripal sites focused on crop and breeding research. DEVELOPMENT VERSION. DivSeek Canada Pilot Project: Harnessing Genomics to Accelerate Crop Improvement in Canada.