Central repository for containers used in the Microbiome Informatics Team at EMBL - EBI

Using the Taskfile

This repository uses Task to simplify building and managing container images.

Prerequisites

• Docker with buildx support
• Taskfile.dev installed (see https://taskfile.dev/installation/)

Available Commands

Building Images

To build a container image locally for a specific tool and version:

task build TOOL=mgnify-pipelines-toolkit VERSION=1.4.9

This command builds a multi-platform image (linux/amd64 and linux/arm64) from the Dockerfile located in mgnify-pipelines-toolkit/1.4.9/. The image is tagged as quay.io/microbiome-informatics/mgnify-pipelines-toolkit:1.4.9.

Building and Pushing Images

To build and push an image directly to the Quay.io registry:

task build-push TOOL=mgnify-pipelines-toolkit VERSION=1.4.9

This performs the same build process but additionally pushes the resulting image to the registry. You must be authenticated to the quay.io/microbiome-informatics organization.

Listing Available Tools

To see all available tools and versions in the repository:

task list

This scans the directory structure and displays all tools with their available versions.

Repository Structure

Each tool is organized in the following structure:

tool-name/
└── version/
    └── Dockerfile

For example, mgnify-pipelines-toolkit/1.4.9/Dockerfile contains the build instructions for version 1.4.9 of the MGnify Pipelines Toolkit.

Image Registry

All images are pushed to the Quay.io registry under the microbiome-informatics organization. Images are available at quay.io/microbiome-informatics