README.md

Sanger Sequencing

Supports integration with Sanger Sequencing research equipment. As a user, I can place an order and specify samples. Samples are grouped together into submissions (one per order detail).

As a facility admin, I can group submissions into a batch and arrange multiple submissions on a well plate. As a facility admin, I can download a CSV that corresponds to the submission layouts on the well plate. As a facility admin, I can upload the CSV to the Sanger machine. (outside of NUCore) As a facility admin, I can upload the test results in NUCore and attach them to the relevant batch.

As a user, I can download my test results when they are ready.

Enabling Sanger Sequencing

Turn on the engine

Make sure the engine is enabled in your Gemfile

gem "sanger_sequencing", path: "vendor/engines/sanger_sequencing"

Enable the admin-tab for the facility

There is not currently an interface for enabling the admin-side management. In order to enable the "Sanger" top-level tab for a facility, set the sanger_sequencing_enabled field to true/1 on the facility in the facilities table. From the rails console, you can do this by:

Facility.find_by(url_name: "facility-name").update(sanger_sequencing_enabled: true)

Set up the order form for a service

• Create a new service from the Products tab, including Pricing
• Under "Order Forms", add a new Online Order Form
• Use the URL https://[yourdomain]/sanger_sequencing/submissions/new and click "Add"
• Click "Activate" to turn it on

Enable Fragment Analysis Well Plate Creation

• Create a Fragment Analysis Product

• Add a row "fragment" under sanger_sequencing_product_groups that maps to the new product.

  SangerSequencing::ProductGroup.create(product: product, group: "fragment")

A product can only be part of a single group. If it is not part of a group, it falls back to a "default" group, which is the standard Sanger Sequencing.