chanzuckerberg / shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
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Support for macOS 11 (Big Sur) #229

Closed paoloczi closed 3 years ago

paoloczi commented 3 years ago

Currently the Shasta macOS build is done on macOS 10.15, and that build works on both macOS 10.15 and 10.14. However it does not work on macOS 11 (Big Sur). We need a port of Shasta to macOS 11. This requires:

If somebody decides to take over this port, I will help - however I have no knowledge of macOS nor a macOS machine to test on. Please comment here to communicate issues that you bump into or questions you may have.

AustinHartman commented 3 years ago

I was able to build locally and run a small assembly on macOS 11. Generating a local build only required switching off the spoa_optimize_for_native option. However, I ran into an issue when adding the build step. It seems that macOS 11 virtual environments are not available at the moment (see the note here: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobsjob_idruns-on)

paoloczi commented 3 years ago

Thank you sou much for looking at this - this is good to know. So it seems that we can support macOS 11 as soon as GitHub Actions allows macOS 11 builds.

I assume your test was on Intel hardware - correct? A separate build will be needed to build for Apple ARM hardware. Presumably GitHub Actions will provide a second environment for that.

paoloczi commented 3 years ago

If you create a PR with just the changes needed to build, and without the new GitHub Actions job, I will merge it.

Or perhaps include in the PR the new GitHub Actions job, but commenting it out. That way it will be easy to activate when the new environment becomes available, and in the meantime people will be able to build it themselves.

AustinHartman commented 3 years ago

Actually my local build and test was on ARM hardware. Unfortunately, I don't have access to macOS 11 machine using intel hardware, so I'm unable to test that - hopefully GHA provide an environment for each. For now, I'll open a PR with the changes which allowed me to build locally.

paoloczi commented 3 years ago

After PR #242, Shasta builds on macOS 11 - at least the ARM version. Thank you @AustinHartman for that!

The PR also includes changes in the Github Actions workflow to do regular macOS 11 test builds , but those are turned off due to lack of support from GitHub. Therefore the build is subject to breakage during development.