new-image

name	new-image
description	Create a new Docker image for a bioinformatics tool
argument-hint	<tool-name>
allowed-tools	Bash, Read, Glob, Grep, WebSearch, WebFetch

Create a New Docker Image

Scaffold and build a new WILDS Docker image for an open-source bioinformatics tool.

Steps

1. Research the Tool

Before writing any files, research the tool to understand:

• What it does and what it is used for
• The latest stable version available
• How it is typically installed (apt, conda/mamba, pip, compiled from source, pre-built binary/JAR, etc.)
• What base image is most appropriate (ubuntu:24.04, condaforge/miniforge3, bioconductor/bioconductor_docker, python:3.x-slim, etc.)
• Its official homepage and citation information
• What dependencies it requires

2. Create the Tool Directory and Dockerfile

• Create a new directory named after the tool (lowercase, hyphens for multi-word names)
• Read template/Dockerfile_template first as the formatting reference
• Create Dockerfile_latest following ALL Dockerfile requirements from AGENTS.md:
  • OCI metadata labels (title, description, version, authors, source URL, MIT license)
  • SHELL ["/bin/bash", "-o", "pipefail", "-c"]
  • Pinned versions for system packages using apt-cache policy
  • A smoke test RUN command verifying the install (e.g., tool --version)
  • Cleanup steps (rm -rf /var/lib/apt/lists/*, mamba clean -afy, remove tarballs, etc.)
• Also create Dockerfile_X.Y.Z for the specific version (may be identical to latest)
• Target image size: a few hundred MB, max 2GB. One primary tool per image.

3. Create the README

• Read template/README.md first as the formatting reference
• Fill in all standard sections: description, available versions, image details, citation, Docker/Apptainer usage, example commands, Dockerfile structure, security/CVE info, and source repository
• Remove any optional sections that do not apply
• Remove ALL HTML comments and template instructions from the final README
• Provide realistic example commands

4. Lint the Dockerfile

Run make lint IMAGE=<toolname> to check for hadolint issues. Fix any warnings or errors before proceeding.

5. Build and Test

Run make build_amd64 IMAGE=<toolname> to verify the image builds successfully. Diagnose and fix any failures, then re-run until it passes.

6. Summary

After all steps pass, report:

• The tool version packaged
• The base image used
• The installation method chosen
• Any notable decisions or trade-offs made
• Confirmation that lint and build passed