Images

This is a repository of:

• Single-software images to build and push in the cpg-common artifact registry.
• Scripts that move external images into our artifact registry using skopeo.

This is a BAD place for:

• multi-software images
• analysis-specific images, e.g., an image that contains an in-progress script for processing data

Single tool images

Assuming you want to create an image for a tool called mytool of version 1.0.1, add a folder called images/mytool with a Dockerfile file. Parametrise the Dockerfile by ${VERSION} that will correspond to the version of your tool and the tag of your future image. For example, inside the Dockerfile you would have:

ARG VERSION=${VERSION}
RUN pip install mytool==${VERSION}

Then, add an entry into images.toml with the name of your image matching the desired tag/version:

mytool = '1.0.1'

Finally, create a pull-request with your changes and assign someone to review it. Once merged, the GitHub CI will automatically build your image and push it into the cpg-common artifact registry.

To update the tool version, modify the corresponding entry in TOML and create a pull request, CI will automatically rebuild the image.

Image moving scripts

Whenever possible, avoid moving images with scopeo, and build them with a Dockefile instead following the section above. Moving is not recommended for two reasons:

• It hides how the image was build originally (and sometimes the original Dockefile is not even shared),
• The source image can be removed by the author in the future, making your analysis no longer reproducible.

If you still need to move, create a script named move-{IMAGE_NAME}:{IMAGE_VERSION}.sh following the template below:

#!/usr/bin/env bash
set -ex
SOURCE_IMAGE=""
IMAGE_NAME=""
IMAGE_TAG=""

gcloud auth configure-docker australia-southeast1-docker.pkg.dev
skopeo copy ${SOURCE_IMAGE} docker://australia-southeast1-docker.pkg.dev/cpg-common/images/${IMAGE_NAME}:${IMAGE_TAG}

And submit it with the analysis runner:

IMAGE_NAME="mytool"
IMAGE_TAG="1.0.1"
analysis-runner \
    --dataset fewgenomes --access-level standard \
    --description "Images: Move ${IMAGE_NAME}:${IMAGE_TAG}" \
    --output-dir images/mv-${IMAGE_NAME}-${IMAGE_TAG} \
    scripts/move-${IMAGE_NAME}:${IMAGE_TAG}.sh