Container images for bioinformatics tools

This repository provides a simple, reproducible way to build, test and push Docker/OCI images for the following command‑line utilities:

Tool	Description	Versions
clinker	Gene cluster comparison and visualisation (clinker-py)	0.0.12, 0.0.19 – 0.0.32
cblaster	Remote homologue detection and gene cluster search (ships with cagecleaner)	1.3.9, 1.3.11 – 1.3.20, 1.4.0
defense‑finder	Systematic search for anti‑phage defense systems	1.0.9, 1.1.1, 1.2.0 – 1.2.2, 1.3.0, 2.0.0, 2.0.1
rgi	Resistance Gene Identifier (CARD)	5.0.0, 5.1.0 – 5.2.1, 6.0.0 – 6.0.5

All tools are installed from the Bioconda package channel using micromamba running on an Alpine base image. The resulting containers are small and suitable for use in pipelines, Kubernetes jobs, or as base images for other workflows.

Repository layout

/
├─ clinker/
│  ├─ 0.0.12/Dockerfile
│  ├─ 0.0.19/Dockerfile
│  └─ ...
├─ cblaster/
│  ├─ 1.3.9/Dockerfile
│  ├─ 1.3.11/Dockerfile
│  └─ ...
├─ defense-finder/
│  ├─ 1.0.9/Dockerfile
│  ├─ 2.0.1/Dockerfile
│  └─ ...
├─ rgi/
│  ├─ 5.0.0/Dockerfile
│  ├─ 6.0.5/Dockerfile
│  └─ ...
├─ tests/
│  ├─ clinker/test.sh
│  ├─ cblaster/test.sh
│  ├─ defense-finder/test.sh
│  └─ rgi/test.sh
├─ .github/
│  ├─ workflows/build-container.yml        # CI workflow
│  └─ dependabot.yml                       # dependency updates
└─ README.md

Each version directory contains a nearly‑identical Dockerfile that parameterises the package version via an ARG. New releases can be added simply by creating a new directory and copying one of the existing Dockerfiles, then updating the ARG value.

Building locally

You can build an image manually with docker build or podman:

docker build -t clinker:0.0.32          ./clinker/0.0.32
docker build -t cblaster:1.4.0          ./cblaster/1.4.0
docker build -t defense-finder:2.0.1    ./defense-finder/2.0.1
docker build -t rgi:6.0.5               ./rgi/6.0.5

Replace the tool name and version string as needed. The containers rely only on the packages installed by micromamba, so no additional build dependencies are required.

Testing locally

Each tool has a test suite under tests/<tool>/test.sh. The script expects two arguments: the image reference and the expected version.

docker build -t test/clinker:0.0.32 ./clinker/0.0.32
tests/clinker/test.sh test/clinker:0.0.32 0.0.32

Continuous Integration

A single GitHub Actions workflow (.github/workflows/build-container.yml) runs on every push to main and on pull requests that touch a Dockerfile or a test script. The logic is as follows:

1. A detect‑changes job determines which tool/version pairs are affected using git diff:
   • A changed Dockerfile → build, test, and push that specific version.
   • A changed test script → build and test all versions of that tool, but no push.
   • If nothing is affected the workflow exits early.
2. A build job uses a dynamic matrix of affected versions. For each entry it:
   • Builds the image locally
   • Runs the functional test suite against it
   • Pushes the image to GHCR only when the Dockerfile changed and the event is a push to main

The workflow also supports manual invocation via workflow_dispatch, which rebuilds, tests, and pushes every image.

Dependency updates

A dependabot.yml configuration keeps the GitHub Actions and the base images up to date. Pull requests are opened weekly whenever new versions are available; they are labeled dependencies and either github-actions or docker.

Contributing

1. Create a new <tool>/<version>/Dockerfile directory (copy an existing one and update the ARG).
2. Add or update the test script in tests/<tool>/test.sh.
3. Build and test locally to verify.
4. Commit and push; the CI will test and publish images automatically.

License & Attribution

This repository does not contain the tools themselves, which are distributed under their respective licenses. The container definitions are provided under the MIT License.

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Maintained by exTerEX