Conda build for macos

[jodyphelan]

I saw clair3 is now natively supported on apple silicon. Will it also be available on conda for macos?

[zhengzhenxian]

We tested and found that using brew installation is more stable than conda. Some packages, such as samtools and pypy3, can occasionally fail during installation with conda.

[jodyphelan]

Ok thanks!

[BioWilko]

I understand that brew is better but I use clair3 as a dependency so it not being available on bioconda means my whole pipeline cannot run natively on apple silicon, would you consider allowing bioconda builds with some sort of notice explaining your concerns with it?

[aquaskyline]

Understood, but to solve your problem, more likely we will create a new package named Clair3-applesilicon, which will not be updated as frequently as Clair3. The fact is that tweaking the dependencies in macOS is still cumbersome, and we can only afford so much engineering work.

[BioWilko]

I understand not having enough resources to maintain everything (I have too much to maintain myself), so long as Clair3-applesilicon builds for amd64 and aarch64 I think that would work great!

[aquaskyline]

What I am thinking is that Clair3-applesilicon only builds for aarch64. Does conda support choosing between receipts according the current platform?

[BioWilko]

I'm not sure, @rpetit3 is this possible?

[rpetit3]

Hi all!

I think this might be possible using [arm64], [aarch64], [x86_64] like the following: https://github.com/bioconda/bioconda-recipes/blob/28dc99e6ee493d1979356f4799dece8b715cd7fd/recipes/deltapd/meta.yaml#L19-L21

    - sed -i.bak 's|-march=native|-march=armv8-a|' setup.py  # [aarch64]
    - sed -i.bak 's|-march=native|-march=armv8.4-a|' setup.py  # [arm64]
    - sed -i.bak 's|-march=native|-march=x86-64-v3|' setup.py  # [x86_64]

@aquaskyline - I'd recommend trying this approach before creating a new recipe. Because then no recipes that depend on claire would need to be changed.

Otherwise @BioWilko you would need to update your decipe to something like

run:
...
  - claire3 [x86_64 or aarch64]
  - claire3-applesilicon [arm64]

Again, I would recommend trying to make the changes into clair3's current recipe before branching out to additional build specific recipes.

Cheers,
Robert

[aquaskyline]

@rpetit3 Thanks Robert, very helpful! Will give a solution in the next release.

[rpetit3]

Sounds good @aquaskyline let me know if I can help on the bioconda side of things

[jodyphelan]

I'm no conda packaging expert but I'm also happy to test things!