k-8, python >=3.8 and osx x86_64

[lynnjo]

This is a follow up to the closed issue 50888 (#50888)

Has any progress been made to make k8 to build on python >=3.8 for osx x86_64? We are still in need of this for our pipeline. Thanks - Lynn

[martin-g]

Has any progress been made to make k8 to build on python >=3.8 for osx x86_64?

No!
Help is welcome!

[lynnjo]

@martin-g What sort of issues were you seeing with the osx x86_64 build? Lookin at notes from the previous issue I see k8 needed a different version of v8/Node.js for Linux and OSX. If I read the comments correctly, this was fixed for Linux, Linux ARM, and OSX ARM. Just not for OSX _x86_64. Is that correct?

I honestly don't know what to setup to run your tests that have k8 with minimap2 and python, and probably don't have permissions to retest your CI tests that fail.

[martin-g]

You could open a PR for k8 and/or minimap2 and experiment. The CI checks will give you the feedback.

[lynnjo]

To open a PR I probably need to change something. I have no idea what is wrong so no idea what to change.

I tried pulling the bioconda-recipes code to my iMac and running locally as defined by the instructions below to see what failed:
https://bioconda.github.io/contributor/building-locally.html

However, since I made no changes, nothing was done. I get this message.

(bioconda) rs-btbd1ylcj34:bioconda-recipes lcj34$ bioconda-utils build --docker --mulled-test --git-range master
09:17:27 BIOCONDA INFO Considering total of 9714 recipes.
09:17:27 BIOCONDA INFO Constraining to 0 git modified recipes.
09:17:27 BIOCONDA INFO Processing 0 recipes.
09:17:27 BIOCONDA INFO Using docker image quay.io/bioconda/bioconda-utils-build-env-cos7:3.5.0 for building.
09:17:27 BIOCONDA INFO Nothing to be done.
(bioconda) rs-btbd1ylcj34:bioconda-recipes lcj34$

If you could provide any kind of information on what to be looking at I might be able to test and debug, but currently I'm at a standstill with this.

[lynnjo]

Oh - just saw @mencian note above, so perhaps he is looking at this - thanks!

[mencian]

@lynnjo Please give the new macOS build a try!

[lynnjo]

Has this been delivered ? I am still getting an error message.

My environment.yml file looks like:

name: phgv2-updatedTiledb
channels:

• conda-forge
• bioconda
• tiledb
  dependencies:
• python=3.10
• tiledb-py=0.32.0
• tiledbvcf-py=0.35.0
• anchorwave=1.2.5
• bcftools
• samtools
• agc=3.1
• minimap2=2.28

My command is:
conda env create --solver libmamba -f upgraded_environment.yml

The error is:

conda env create --solver libmamba -f upgraded_environment.yml
Retrieving notices: ...working... done
Channels:

• conda-forge
• bioconda
• tiledb
• defaults
  Platform: osx-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed
  Channels:
• conda-forge
• bioconda
• tiledb
• defaults
  Platform: osx-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• package libtiledbvcf-0.35.0-hfffce77_0 requires tiledb >=2.26.0,<2.27.0a0, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ minimap2 2.28** is installable with the potential options
│ ├─ minimap2 2.28 would require
│ │ └─ libzlib >=1.2.13,<1.3.0a0 , which can be installed;
│ └─ minimap2 2.28 would require
│ └─ k8 with the potential options
│ ├─ k8 0.2.5 would require
│ │ └─ zlib >=1.2.11,<1.3.0a0 , which can be installed;
│ ├─ k8 0.2.5 would require
│ │ └─ zlib >=1.2.13,<1.3.0a0 , which can be installed;
│ ├─ k8 0.2.5 would require
│ │ └─ libzlib >=1.2.13,<1.3.0a0 , which can be installed;
│ ├─ k8 [1.0|1.1|1.2] would require
│ │ └─ python_abi 3.8.* _cp38 with the potential options
│ │ ├─ python_abi 3.8 would require
│ │ │ └─ python 3.8. , which can be installed;
│ │ └─ python_abi 3.8, which can be installed;
│ └─ k8 1.2 would require
│ └─ python_abi 3.13.* _cp313, which can be installed;
├─ python 3.10* is uninstallable because there are no viable options
│ ├─ python [3.10.0|3.10.10|...|3.10.9] conflicts with any installable versions previously reported;
│ ├─ python [3.10.0|3.10.1|...|3.10.9] would require
│ │ └─ python_abi 3.10.* _cp310, which conflicts with any installable versions previously reported;
│ └─ python [3.10.15|3.10.16] would require
│ ├─ libzlib >=1.3.1,<2.0a0 but there are no viable options
│ │ ├─ libzlib 1.3.1 would require
│ │ │ └─ zlib 1.3.1 _1, which conflicts with any installable versions previously reported;
│ │ ├─ libzlib 1.3.1 would require
│ │ │ └─ zlib 1.3.1 _2, which conflicts with any installable versions previously reported;
│ │ └─ libzlib 1.3.1 would require
│ │ └─ zlib 1.3.1 _0, which conflicts with any installable versions previously reported;
│ └─ python_abi 3.10. _cp310, which conflicts with any installable versions previously reported;
├─ tiledb-py 0.32.0 is installable with the potential options
│ ├─ tiledb-py 0.32.0 would require
│ │ └─ tiledb >=2.26.0,<2.27.0a0 , which requires
│ │ └─ libzlib >=1.3.1,<2.0a0 , which cannot be installed (as previously explained);
│ ├─ tiledb-py 0.32.0 would require
│ │ ├─ python >=3.11,<3.12.0a0 , which can be installed;
│ │ └─ python_abi 3.11. _cp311, which can be installed;
│ ├─ tiledb-py 0.32.0 would require
│ │ └─ python_abi 3.12. _cp312, which can be installed;
│ └─ tiledb-py 0.32.0 would require
│ ├─ python >=3.9,<3.10.0a0 , which can be installed;
│ └─ python_abi 3.9. _cp39, which can be installed;
└─ tiledbvcf-py 0.35.0 is uninstallable because it requires
└─ libtiledbvcf 0.35.0 hfffce77_0, which requires
└─ tiledb >=2.26.0,<2.27.0a0 , which cannot be installed (as previously explained).

If I remove the version specification for python and minimap2 I end up with python 3.12.8 but minimap2, instead of the 2.28 version I'd like, shows up as minimap2.1.1 with 0 as the build. This is the same error I was seeing before.