Template R Operator

The Template R Operator is a template repository for the creation of R operators in Tercen. An overview of steps for developing an operator are:

1. Create a new GitHub repository using this template
2. Clone the newly created repository to your development environment (we recommend using VS Code)
3. Describe your operator specifications in the README file
4. Develop the operator (with or without assistance from the Tercen Agents)
5. Initialise or update the R packages environment using renv.
6. Push your changes and install the operator in Tercen

Detailed information can be found in the Tercen developer's guide.

Setup Checklist

After creating your operator from this template, complete the following steps:

• Update operator.json:
  • Change name and description
  • Update authors to your organization
  • Update container to match your repo: ghcr.io/YOUR_ORG/YOUR_REPO:main
  • Update urls similarly
  • Configure properties for your operator's parameters
• If using minimal base image, uncomment and configure the Dockerfile accordingly
• Run renv::init() locally and commit renv.lock
• Push your changes to trigger the CI workflow
• Important: Make the Docker package publicly accessible (see below)

GitHub Container Registry Visibility

By default, GitHub Container Registry (ghcr.io) packages inherit the repository's visibility settings. If your repository is private, the Docker image will also be private, and Tercen/BioNavigator will fail to pull it with an error like:

Error response from daemon: denied

To fix this, you have two options:

1. Make the package public (recommended if repo stays private):

   • Go to https://github.com/orgs/YOUR_ORG/packages
   • Find your operator package
   • Click "Package settings"
   • Under "Danger Zone", click "Change visibility" and select "Public"

2. Make the repository public:

   • This automatically makes associated packages public

Dockerfile Options

This template provides two base image options:

Option	Base Image	Use Case
Full runtime (default)	tercen/runtime-r44:4.4.3-8	Most dependencies included, easier setup
Minimal runtime	tercen/runtime-r44-minimal:4.4.3-2	Smaller image, requires adding build dependencies

If using the minimal runtime, uncomment the relevant lines in the Dockerfile and add any system dependencies your R packages require. Common dependencies:

• gcc g++ musl-dev make - C/C++ compilation (most R packages)
• gfortran - Fortran compiler (statistical packages, linear algebra)
• curl-dev openssl-dev - HTTP/SSL support
• cargo rust - Rust toolchain (some modern R packages)
• build-base linux-headers libxml2-dev - Required for installing R packages from GitHub that need compilation (e.g., pamgene packages)

Git LFS

This template includes a .gitattributes file with commented-out LFS tracking rules for common large file types (.rds, .csv, .pdf, images). If your operator requires large data files:

1. Install Git LFS: git lfs install
2. Uncomment the relevant lines in .gitattributes for file types you need to track
3. Run git lfs track to verify your patterns
4. Commit the updated .gitattributes before adding large files

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Below is the operator README standard structure.

Description

The Template R operator is a template repository for the creation of R operators in Tercen.

Usage

Input	.
x-axis	type, description
y-axis	type, description
row	type, description
column	type, description
colors	type, description
labels	type, description

Settings	.
input_var	parameter description

Output	.
output_var	output relation
Operator view	view of the Shiny application

Details

Details on the computation.