It is recommended to clear cashes regularly in this installation processes.
The package is available as one repository for Pulse Bioinformatics, University of Saskatchewan on GitHub. Recommended method of downloading and installation is using git:
cd [your drupal root]/sites/all/modules git clone https://github.com/UofS-Pulse-Binfo/kp_germplasm.git
The module can be enabled in “Home » Administration » Tripal » Modules” by select the checkbox under “ENABLED” column (as shown in above image) and then click on “Save Configuration” button by the bottom of page.
Another method that can enable our module is using drush:
drush pm-enable kp_germplasm drush pm-enable rilsummary germpcollection
In this step, module required ontologies and controlled vocabularies will be inserted into Chado. Make sure to run any Tripal jobs created by these modules before continuing.
By default, permission of using both importers in this module is not set. It can be configured in “Home » Administration » People » Permissions”.
After the module is installed and enabled, both Germplasm Cross Importer and Germplasm Accession Importer should be ready to use in “Home » Administration » Tripal » Data Loader”.
For more information on the importers, See the Data Import section of these docs.
The importers add data to from your file into Chado. You then need to publish that data by going to Admin > Content > Tripal Content > Publish and selecting either “F1” for crosses or “Germplasm Accessions”.
Upgrade path from Separate Modules¶
This package includes modules which used to stand alone (germ_summary, tripal_germplasm_importer, germcollection). To upgrade,
- Take note of any existing configuration both in Tripal > Extensions and Structure > Tripal Content Types.
- Disable and uninstall the existing modules. This will not delete any data in chado; however, you will need to re-configure the functionality.
- Remove the old module directories.
- Clone this package and re-install the modules
- Re-apply the configuration you took note of above.
You may need to re-configure after upgrading to this package so take careful note of your original configuration.
The functionality from separate modules will still be available in this package and any new functionality will be developed here. Additionally, germ_summary has been renamed to rilsummary to reflect it’s focus on RILs.