HolobiomicsLab tima-entry-point-validation
Summary
Verify that a tima Docker container (adafede/tima-r) successfully pulls from Docker Hub and launches without errors, confirming the container's entry point is accessible and functional.
When to use
When you have obtained or are considering use of the tima Docker image (adafede/tima-r) and need to confirm that the containerized environment is operational before proceeding with metabolite annotation workflows. This is a smoke test to catch environment or registry issues early.
When NOT to use
- You are using a native R installation of tima instead of a container — use R package import validation instead.
- You have already validated the container in a previous step in the same workflow — do not repeat unnecessarily.
- Docker is not available or Docker daemon is not running in your environment.
Inputs
- Docker Hub registry URL (adafede/tima-r)
- Docker daemon (local or remote)
Outputs
- Pulled Docker image (adafede/tima-r)
- stdout/stderr from tima help or version command (text output confirming functional entry point)
How to apply
Pull the Docker image adafede/tima-r from Docker Hub using docker pull. Launch a container instance from the pulled image. Execute a tima help or version command within the running container to confirm the entry point is accessible and functional. A successful invocation should return version information or help text without errors, confirming the R environment and tima package are correctly installed and callable within the container.
Related tools
- Docker (Container platform used to pull and launch the tima-r image) — https://www.docker.com/
- tima-r Docker image (Containerized R environment with tima package and dependencies pre-installed) — https://hub.docker.com/r/adafede/tima-r/
- tima (R package executed within the container to validate entry point functionality) — https://github.com/taxonomicallyinformedannotation/tima
Examples
docker pull adafede/tima-r && docker run --rm adafede/tima-r R --version
Evaluation signals
- docker pull command completes without 'manifest not found' or authentication errors
- docker run successfully creates and starts a container instance without immediate exit or crash
- tima help or version command executes within container and returns non-empty output
- Command exit code is 0 (success), not a non-zero error code
- No errors related to missing R packages, library linking, or entry point are reported in stderr
Limitations
- This smoke test validates only the container's basic operability and R environment; it does not validate the correctness of tima's underlying algorithms or dependencies (e.g., SIRIUS, GNPS libraries).
- Network access to Docker Hub is required to pull the image; offline environments or restricted registries will fail.
- The test does not verify data input/output workflows or the Shiny app interface (
run_app()) — only the CLI entry point.
Evidence
- [other] Does the tima Docker container (adafede/tima-r) successfully pull and launch without errors?: "Does the tima Docker container (adafede/tima-r) successfully pull and launch without errors?"
- [other] Workflow steps from task_003: "1. Pull the Docker image adafede/tima-r from Docker Hub using docker pull. 2. Launch a container instance from the pulled image. 3. Execute a tima help or version command within the running container"
- [readme] Docker badge and availability: ""
- [readme] Docker pull and launch instructions from README: "docker pull adafede/tima-r"