Loosen constraints for bcftools, samtools, and bwa for compatibility …

[clelange]

…with Apple Silicon

Fixes #14

Summary by CodeRabbit

• Chores
  • Updated dependency version requirements for bcftools, samtools, and bwa to support a broader range of releases, ensuring improved compatibility and smoother future updates.
  • Changed environment management commands from mamba to conda in the Dockerfile for consistency.

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request modifies the environment.yaml file to change the version specifications for the dependencies bcftools, samtools, and bwa. The fixed version constraints have been updated to allow for more flexibility, permitting any version greater than or equal to the specified minimum for bcftools and samtools, and any compatible version for bwa. Additionally, the Dockerfile has been updated to replace mamba with conda for environment management commands.

Changes

File	Change Summary
environment.yaml	Updated dependency version specifications: bcftools from 1.19 to >=1.19; samtools from 1.19.2 to >=1.19; bwa from 0.7.17 to ~=0.7.17.
Dockerfile	Replaced mamba commands with conda for creating and updating the environment.

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• Dockerfile (1 hunks)

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• GitHub Check: test

🔇 Additional comments (1)

Dockerfile (1)

3-4: Switch to conda for environment management

The updated commands replacing mamba with conda in lines 3-4 align well with the PR objective of enhancing compatibility with Apple Silicon. Using conda create ... --clone snakemake and conda env update is appropriate in this context. Please ensure that the conda channels and environment configurations remain optimal for performance and that the --clone option replicates the expected base environment correctly.

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[clelange]

On Apple Silicon, this then yields the following packages:

❯ pixi list --explicit
Package            Version  Build            Size       Kind   Source
bcftools           1.21     h48e1df0_1       875.7 KiB  conda  https://conda.anaconda.org/bioconda/
bwa                0.7.18   hba9b596_2       202.7 KiB  conda  https://conda.anaconda.org/bioconda/
graphviz           12.2.1   hff64154_1       2.1 MiB    conda  https://conda.anaconda.org/conda-forge/
jinja2             3.1.6    pyhd8ed1ab_0     110.1 KiB  conda  https://conda.anaconda.org/conda-forge/
matplotlib         3.10.1   py312h1f38498_0  16.7 KiB   conda  https://conda.anaconda.org/conda-forge/
pygments           2.19.1   pyhd8ed1ab_0     867.8 KiB  conda  https://conda.anaconda.org/conda-forge/
pysam              0.22.0                    37.9 MiB   pypi   pysam-0.22.0-cp312-cp312-macosx_11_0_arm64.whl
samtools           1.21     h267f7b9_1       449.6 KiB  conda  https://conda.anaconda.org/bioconda/
snakemake-minimal  8.29.3   pyhdfd78af_0     821.3 KiB  conda  https://conda.anaconda.org/bioconda/

[clelange]

The test failures are not due to this change, but due to mamba missing:

#8 [3/4] RUN mamba create -n snakemake-tutorial --clone snakemake;     mamba env update -n snakemake-tutorial -f environment.yaml;
#8 0.172 bash: line 1: mamba: command not found
#8 0.172 bash: line 1: mamba: command not found
#8 ERROR: process "/usr/local/bin/_dockerfile_shell.sh mamba create -n snakemake-tutorial --clone snakemake;     mamba env update -n snakemake-tutorial -f environment.yaml;" did not complete successfully: exit code: 127

[clelange]

Once #17 is in, I can rebase.

[cmeesters]

ok, trivial