use docker multi-stage build

[bpow]

This reduces the docker image size from ~1.19GB to ~43MB, for approximately 96% savings!

Even better (from reproducibility standpoint) would be to build from something more formally-specified than brentp/musl-hts-nim:latest, and potentially more up-to-date, but with quick look some of the static libraries (e.g., for openmp/blas) wouldn't necessarily be available in a newer alpine version.

[gemini-code-assist]

Hello @bpow, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

Summary of Changes

This pull request implements a multi-stage Docker build to significantly reduce the final image size for the somalier tool. The image size is reduced from approximately 1.19GB to approximately 43MB, achieving a 96% reduction. The first stage builds the somalier executable, and the second stage copies the executable and necessary files into a smaller Alpine Linux base image.

Highlights

• Docker Multi-Stage Build: The Dockerfile is updated to use a multi-stage build, leveraging a build stage based on brentp/musl-hts-nim:latest to compile somalier and a final stage based on alpine:3.21 to create a smaller image.
• Image Size Reduction: The primary goal is to reduce the Docker image size, which is achieved by copying only the necessary artifacts (the somalier executable and the ancestry labels file) to the final image.

Changelog

• docker/Dockerfile
  • The base image for the build stage is set to brentp/musl-hts-nim:latest and aliased as build.
  • The apk add bash procps command is removed from the first stage.
  • The somalier executable is compiled in the build stage.
  • A new stage is introduced based on alpine:3.21.
  • The apk add --no-cache bash procps command is added to the new stage.
  • The somalier executable and ancestry-labels-1kg.tsv are copied from the build stage to the new stage.
  • The rm -rf /somalier && somalier --help command is removed.
  • The somalier_ancestry_labels environment variable is updated to use an equals sign.

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[gemini-code-assist]

Code Review

This pull request introduces a multi-stage Docker build to significantly reduce the image size of the somalier tool. This is a great improvement for distribution and deployment. The changes look good overall, but I have a few suggestions for clarity and best practices.

Merge Readiness

The changes in this pull request are a significant improvement, reducing the Docker image size substantially. I recommend merging this pull request after addressing the comments provided, particularly the one regarding explicitly setting the working directory in the second stage. I am unable to directly approve this pull request, and recommend that others review and approve this code before merging.

[gemini-code-assist]

It's good practice to explicitly set the working directory in each stage of a multi-stage build. This ensures that subsequent commands are executed in the correct context, regardless of the previous stage's state. Consider adding WORKDIR /app (or similar) after the FROM alpine:3.21 instruction.

FROM alpine:3.21
WORKDIR /app

[bpow]

The workdir isn't needed here since all of the commands afterwards either write to "system" directories (apk) or involve fully-specified paths.

Nevertheless, under the principle that "explicit is better than implicit", I've force-pushed the commit setting workdir to / in case there are future modifications to the dockerfile that would benefit from this being set.

[brentp]

thank you!