Available Packages on Bioconda

Oct 13, 2025 by sorusgentrification.com 94 views

Introduction

The increasing adoption of Apple Silicon has led to a growing need for optimized packages that can run seamlessly on these systems. However, the current package constraints for popular bioinformatics tools such as bcftools, samtools, and bwa are too tight, limiting their compatibility with Apple Silicon. In this article, we will explore the available packages on bioconda, discuss the current constraints, and propose an update to these constraints to ensure better compatibility with Apple Silicon.

Available Packages on Bioconda

Bioconda is a popular package repository that provides a wide range of bioinformatics tools and libraries. We can use the pixi command to search for packages on bioconda. Let's take a look at the available packages for bcftools, samtools, and bwa.

Bcftools

❯ pixi search bcftools
Using channels: conda-forge, bioconda

bcftools-1.21-h48e1df0_1 (+ 1 build)
------------------------------------

Name                bcftools
Version             1.21
Build               h48e1df0_1
Size                896725
License             GPL
Subdir              osx-arm64
File Name           bcftools-1.21-h48e1df0_1.tar.bz2
URL                 https://conda.anaconda.org/bioconda/osx-arm64/bcftools-1.21-h48e1df0_1.tar.bz2
MD5                 167c52c67c36b990d162f926c4a1b17f
SHA256              9579f70324ed346e9a3b44ad2bf21b381494a6235eb8d035b29a04331509dafa

Dependencies:
 - gsl >=2.7,<2.8.0a0
 - htslib >=1.21,<1.22.0a0
 - libzlib >=1.3.1,<2.0a0
 - perl

Other Versions (1):
Version  Build
1.20     h82beb8a_1

Samtools

❯ pixi search samtools
Using channels: conda-forge, bioconda

samtools-1.21-h267f7b9_1 (+ 1 build)
------------------------------------

Name                samtools
Version             1.21
Build               h267f7b9_1
Size                460358
License             MIT
Subdir              osx-arm64
File Name           samtools-1.21-h267f7b9_1.tar.bz2
URL                 https://conda.anaconda.org/bioconda/osx-arm64/samtools-1.21-h267f7b9_1.tar.bz2
MD5                 3160af55371e4b6d89c284efc5eb6c2b
SHA256              d968e5992749fd3939b9f8a3e2e728e762643d5e93e425d9e13a838e31e3e7f1

Dependencies:
 - htslib >=1.21,<1.22.0a0
 - libzlib >=1.3.1,<2.0a0
 - ncurses >=6.5,<7.0a0

Other Versions (2):
Version  Build
1.20     hc9c1273_1
0.1.18   h267f7b9_14

Bwa

❯ pixi search bwa
Using channels: conda-forge, bioconda

bwa-0.7.18-hba9b596_2 (+ 1 build)
---------------------------------

Name                bwa
Version             0.7.18
Build               hba9b596_2
Size                207531
License             GPL3
Subdir              osx-arm64
File Name           bwa-0.7.18-hba9b596_2.tar.bz2
URL                 https://conda.anaconda.org/bioconda/osx-arm64/bwa-0.7.18-hba9b596_2.tar.bz2
MD5                 64ba84e69db0e651796c35e8f1f0755d
SHA256              d5fea5ee50e9d6e3b68aa61f1d2d6d799b27c89b0f89e6c366600696157f9a0c

Dependencies:
 - libzlib >=1.3.1,<2.0a0
 - perl

Current Constraints

The current constraints for these packages are too tight, limiting their compatibility with Apple Silicon. For example, the bcftools package has a constraint of >=1.21, which means that only versions 1.21 and above are allowed. However, the latest version of bcftools available on bioconda is 1.21, which may not be compatible with Apple Silicon.

Similarly, the samtools package has a constraint of >=1.21, which means that only versions 1.21 and above are allowed. However, the latest version of samtools available on bioconda is 1.21, which may not be compatible with Apple Silicon.

The bwa package has a constraint of ~=0.7.17, which means that only versions 0.7.17 and above are allowed. However, the latest version of bwa available on bioconda is 0.7.18, which may not be compatible with Apple Silicon.

Proposed Update

To ensure better compatibility with Apple Silicon, we propose updating the constraints for these packages as follows:

bcftools = ">=1.19"
samtools = ">=1.19"
bwa = "~=0.7.17"

This update will allow for more flexibility in the versions of these packages that are allowed, which should improve their compatibility with Apple Silicon.

Conclusion

In conclusion, the current package constraints for bcftools, samtools, and bwa are too tight, limiting their compatibility with Apple Silicon. We propose updating these constraints to ensure better compatibility with Apple Silicon. This update will allow for more flexibility in the versions of these packages that are allowed, which should improve their compatibility with Apple Silicon.

Future Work

We will follow up with a PR to update the constraints for these packages. We will also continue to monitor the compatibility of these packages with Apple Silicon and update the constraints as needed.

References

[1] Bioconda. (n.d.). Bioconda. Retrieved from https://bioconda.github.io/
[2] Snakemake. (n.d.). Snakemake. Retrieved from https://snakemake.github.io/

Introduction

In our previous article, we discussed the current package constraints for popular bioinformatics tools such as bcftools, samtools, and bwa, and proposed an update to these constraints to ensure better compatibility with Apple Silicon. In this article, we will answer some frequently asked questions (FAQs) related to this topic.

Q: Why are the current package constraints too tight for Apple Silicon?

A: The current package constraints are too tight for Apple Silicon because they are based on the assumption that only the latest versions of these packages are compatible with Apple Silicon. However, this is not always the case. Some older versions of these packages may also be compatible with Apple Silicon, but are not allowed by the current constraints.

Q: What are the benefits of updating the package constraints?

A: Updating the package constraints will allow for more flexibility in the versions of these packages that are allowed, which should improve their compatibility with Apple Silicon. This will make it easier for users to install and run these packages on Apple Silicon, and will also make it easier for developers to maintain and update these packages.

Q: How will updating the package constraints affect the compatibility of these packages with Apple Silicon?

A: Updating the package constraints will improve the compatibility of these packages with Apple Silicon by allowing for more flexibility in the versions of these packages that are allowed. This will make it easier for users to install and run these packages on Apple Silicon, and will also make it easier for developers to maintain and update these packages.

Q: What are the potential risks of updating the package constraints?

A: The potential risks of updating the package constraints include the possibility of introducing new bugs or compatibility issues with Apple Silicon. However, these risks can be mitigated by thoroughly testing the updated packages and ensuring that they are compatible with Apple Silicon.

Q: How can users update the package constraints?

A: Users can update the package constraints by installing the latest version of the package manager (e.g. conda) and then updating the package constraints using the conda update command.

Q: How can developers update the package constraints?

A: Developers can update the package constraints by modifying the package metadata to reflect the updated constraints. This can be done using the conda build command.

Q: What is the current status of the package constraints update?

A: The package constraints update is currently in progress. We will continue to monitor the compatibility of these packages with Apple Silicon and update the constraints as needed.

Q: How can users get involved in the package constraints update?

A: Users can get involved in the package constraints update by providing feedback on the updated packages and reporting any issues or bugs that they encounter. Developers can also get involved by contributing to the development of the packages and updating the package metadata to reflect the updated constraints.

Q: What are the next steps for the package constraints update?

A: The next steps for the package constraints update include thoroughly testing the updated packages and ensuring that they are compatible with Apple Silicon. We will also continue to monitor the compatibility of these packages with Apple Silicon and update the constraints as needed.

Q: How can users stay up-to-date with the package constraints update?

A: Users can stay up-to-date with the package constraints update by following the project's blog or social media channels. We will also provide regular updates on the project's website.

Q: What are the benefits of the package constraints update for the bioinformatics community?

A: The package constraints update will benefit the bioinformatics community by improving the compatibility of these packages with Apple Silicon, making it easier for users to install and run these packages on Apple Silicon, and making it easier for developers to maintain and update these packages.

Q: How will the package constraints update affect the bioinformatics community?

A: The package constraints update will have a positive impact on the bioinformatics community by improving the compatibility of these packages with Apple Silicon, making it easier for users to install and run these packages on Apple Silicon, and making it easier for developers to maintain and update these packages.

Q: What are the potential long-term benefits of the package constraints update?

A: The potential long-term benefits of the package constraints update include improved compatibility of these packages with Apple Silicon, improved ease of use for users, and improved maintainability and updateability of these packages for developers.

Q: How can the package constraints update be replicated for other packages?

A: The package constraints update can be replicated for other packages by following a similar process of updating the package metadata to reflect the updated constraints, thoroughly testing the updated packages, and ensuring that they are compatible with Apple Silicon.

Q: What are the potential challenges of replicating the package constraints update for other packages?

A: The potential challenges of replicating the package constraints update for other packages include the possibility of introducing new bugs or compatibility issues, the need for thorough testing and validation, and the need for coordination and communication among developers and users.

Q: How can the package constraints update be scaled up for larger packages?

A: The package constraints update can be scaled up for larger packages by using automated testing and validation tools, by leveraging the expertise of multiple developers and users, and by using cloud-based infrastructure to support the update process.

Q: What are the potential benefits of scaling up the package constraints update for larger packages?

A: The potential benefits of scaling up the package constraints update for larger packages include improved efficiency and productivity, improved accuracy and reliability, and improved scalability and flexibility.

Q: How can the package constraints update be made more transparent and accountable?

A: The package constraints update can be made more transparent and accountable by using open-source tools and methodologies, by providing regular updates and progress reports, and by engaging with the community and soliciting feedback and input.

Q: What are the potential benefits of making the package constraints update more transparent and accountable?

A: The potential benefits of making the package constraints update more transparent and accountable include improved trust and confidence among users and developers, improved collaboration and coordination, and improved overall quality and reliability of the packages.