Add multi-platform SPAdes container support with pigz - #1587
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Build the checked-out SPAdes source in an Ubuntu 24.04 builder and copy only the installed toolkit into the runtime stage. The release project set and NCBI SRA support match the upstream release build configuration.\n\nInstall pigz so corrected-read compression can use the thread count supplied to SPAdes. Run the final image as an unprivileged user from a writable work directory while keeping the full SPAdes toolkit on PATH.\n\nValidation: git diff --cached --check. Image builds and runtime smoke tests are added in the follow-up container CI commit because no local container daemon is available.
Build and load the SPAdes image on native Linux AMD64 and ARM64 GitHub-hosted runners for the same non-documentation events as the existing test suite. Architecture-scoped layer caches reduce repeated source-build cost without publishing an image.\n\nCheck the embedded version, unprivileged writable runtime, pigz availability, absence of build tools, and the bundled SPAdes assembly test. The smoke test also verifies that corrected-read compression selected pigz.\n\nValidation: workflow YAML syntax parsed successfully and git diff --cached --check passed. Runtime validation is performed by this workflow because no local container daemon is available.
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August 1, 2026 13:50
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Hello SPAdes maintainers,
This is intended to supersede #1343. Thank you to @sbassi for proposing the original Dockerfile.
Includes
pigzso SPAdes can use the configured thread count when compressing corrected reads in containerised HPC workloads.CI validates the AMD64 and ARM64 images with the bundled assembly test and confirms that
pigzis selected. The checks are currently awaiting maintainer approval to run.Thank you for maintaining SPAdes and considering this contribution.