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Tercen developer’s guide

6 Deploying an R operator

Now that we have a working R operator for Tercen, we want to deploy it! We will now document, prepare tests and release our linear regression operator.

Documenting the operator

Edit the README.md to describe the operator design and usage. The documentation should contain:

  • A general description of the operator

  • A description of the input projections

  • A description of the output relations

For example, here is how the lm operator documentation looks:

Description

The lm operator performs a linear regression in Tercen.

Usage

Input projection
y-axis measurement value
x-axis explanatory value
Output relations
intercept numeric, intercept of the linear regression, per cell
slope numeric, slope of the linear regression, per cell

Details

The lm operator performs a linear regression on each cell and returns the slope and intercept of the model.

Deploy!

1. Copy the code to the main.R script

Once you are confident enough that your operator is working after testing it locally, you can copy the code to the main.R file.

Make sure not to include the options() calls that are only needed during the local development step:

# The following lines shall not be included into main.R:
options("tercen.workflowId" = "wwww")
options("tercen.stepId"     = "dddd")

getOption("tercen.workflowId")
getOption("tercen.stepId")

2. Initiate renv

The ability to run an operator with exactly the same packages you used when you developed is essential for reproducible science. In order to ensure reproducibility, you can associate packages and their versions to your operator by using the init() function of the renv package:

renv::init()

This will initiate a project-local environment with a private R library in the renv subdirectory.

3. Push it to your GitHub repository

Once everything is ready, you simply need to push all the modifications to the GitHub repository that you created before.

If you want to install it directly from Tercen, you will need to create a release in GitHub.

4. Notify community

Currently, we ask you to send an email to containing the description and link to the operators app git repository, Tercen support will manually test it and add it to the app-library and thus allowing others to access it. We are currently building an web entry point for researchers to browse all the apps offered by the community.