tool_template_r

Template repository for building an R tool that follows the Tool Specification container contract.

How gotap works here

This template installs gotap inside the image and uses it as the default runtime shim:

CMD ["gotap", "run", "foobar", "--input-file", "/in/input.json"]

At build time, gotap generate creates parameters.R from src/tool.yml. At runtime, run.R uses the generated bindings to validate /in/input.json, load parameters and data paths, and write structured run logs.

Required file structure

/
|- in/
|  |- input.json
|- out/
|  |- ...
|- src/
|  |- tool.yml
|  |- run.R
|  |- parameters.R   (generated at build time)
|  |- CITATION.cff

Build and run

Build the image from the template root:

docker build -t tbr_r_template .

Run the sample tool:

docker run --rm -it \
  -v "$(pwd)/in:/in" \
  -v "$(pwd)/out:/out" \
  -e TOOL_RUN=foobar \
  tbr_r_template

TOOL_RUN is only needed when the image contains more than one tool entry.

Customize

1. Update src/tool.yml to describe your tool.
2. Add R or system dependencies in Dockerfile.
3. Implement your tool logic in src/run.R.
4. Rebuild the image so gotap generate refreshes parameters.R.

Generated bindings and logging

The generated parameters.R file is not edited by hand. It exposes:

• get_parameters()
• get_run_context()
• get_logger()

The starter runtime uses get_logger() for structured JSON Lines logging and keeps the sample parsed input visible on standard output.