ARM Documentation updates #16
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I guess we also need add doc in somewhere to mention how to enbale extra:
additional-platforms:
- linux-aarch64 |
Made it more general so it's accurate across multiple CI platforms
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I did a full pass through the docs, doing a lot of cleanup and some organization. Some highlights:
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| This is being initially approached as an opt-in process as we make sure | ||
| all the moving parts are working correctly. A recipe can be flagged for | ||
| building on ``linux-aarch64`` by adding the following to the |
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Do we intend to push containers for that as well? I would like to see this :)
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But not yet? Should we document that? Or should we add an additional key to enable aarch64 containers?
It would be nice to push them if we activate it in the extra section. But I guess that a different discussion.
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I'm actually unclear on the current status of aarch64 containers. I know there was work on getting base images set up, so it could be that aarch64 containers are already handled. I'm still trying to catch up with the recent work though...I'm sure the answer is in there somewhere and once I figure it out I'll clarify this.
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OK, looks like there was some discussion on the core chat (Oct 18) about not immediately uploading aarch64 containers. I think this will be a different discussion. I'll add a note here that containers are currently not built and uploaded.
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Is the core chat public or it is only for the core team ?
I am aware only of https://app.gitter.im/#/room/#bioconda_Lobby:gitter.im but there is no discussion about containers at Oct 18 there.
Thanks!
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I'd also like to join the discussion about aarch64 support! : )
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Yeah, there are many discussions in many places; the one I found re: containers was indeed in a separate core team chat. However we should be better about consolidating information and discussion, ideally on a single github issue.
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@Yikun @martin-g FYI, some recent PRs on pushing aarch64 images to biocontainers: bioconda/bioconda-recipes#43995, bioconda/bioconda-recipes#44457, bioconda/bioconda-utils#941 . . . largely merged into bioconda/bioconda-recipes#40550.
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In thinking about @bgruening's aarch64 container question, I realized I couldn't come up with a clear answer along the lines of, "this specific thing needs to change or be updated in order to fully support aarch64 containers" or "it all looks good". So I took a deep dive into all the containers and wrote up my notes in c69024f. Hopefully this will help inform and clarify future discussions. |
| be installed as a run dependency without having to explicitly add it as such in | ||
| the recipe. This specification is done in the ``zlib`` recipe itself (which is | ||
| hosted by conda-forge), so in general bioconda collaborators can just add | ||
| ``zlib`` as a build dependency. |
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I find this confusing.
https://github.com/bioconda/bioconda-docs/pull/16/files#diff-5a476a141b5805f24f43cab6c3548f1dd1319013abd9035ef91062a6fcd9a35bR441-R442 says that zlib should be in the requirements:host list.
Here the terminology says build dependency which sounds like requirements:build which is only for the compilers, as explained earlier.
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I agree. I think "host dependency" or "host requirement" would be more clear.
Also, I'd like to share my related open PR #18 to clarify how to handle requirements like zlib that use "run exports"
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@jdblischak agreed, and will get to #18 soon. I think this should be fixed over there. Any suggestions on what a better example would be?
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@martin-g thanks again for all the reviews! |
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@daler Thank you for all your work on Bioconda! |
linux-aarch64to all places the supported architectures are mentioned (still waiting for access to Mac M1 on CircleCI)additional-platforms