Installing genome sampler on MacOS running Seqouia

Dear all,

I would love to continue using GenomeSampler for my Phylodynamic analyses. But on my current machine with M2 Ultra ARM64 with macOS Sequoia, it seems impossible to run it. Is the team planning to update GenomeSampler soon ? Are there any specific steps to force install it ? BTW, I managed to install QIIME2. Appreciate the help with this.

when trying to install it, i'm countinously getting this message:

##malkhamis@Mohammads-MacBook-Pro-2 ~ % wget ##https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/conda-env-##files/genome-sampler-py36-osx-conda.yml
#conda env create -n genome-sampler-2020.8 --file genome-sampler-py36-osx-conda.yml
##rm genome-sampler-py36-osx-conda.yml
##--2025-01-29 12:39:47-- https://raw.githubusercontent.com/caporaso-lab/genome-##sampler/r2020.8/conda-env-files/genome-sampler-py36-osx-conda.yml
##Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, ##185.199.111.133, 185.199.109.133, ...
##Connecting to raw.githubusercontent.com ##(raw.githubusercontent.com)|185.199.110.133|:443... connected.

HTTP request sent, awaiting response... 200 OK
Length: 5014 (4.9K) [text/plain]
Saving to: ‘genome-sampler-py36-osx-conda.yml’

genome-sampler-py36-osx-conda.yml 100%[==================================================================>] 4.90K --.-KB/s in 0s

2025-01-29 12:39:48 (10.4 MB/s) - ‘genome-sampler-py36-osx-conda.yml’ saved [5014/5014]

Channels:

The channel is not accessible or is invalid.

You will need to adjust your conda configuration to proceed.
Use conda config --show channels to view your configuration's current state,
and use conda config --show-sources to view config file locations.

Hello @Epidemiologist_GJC,

Platform: osx-arm64

This is the problem. You want osx-64 as the platform/subdir. You can set the subdir to osx-64 within an environment with conda config --set subdir osx-64.

1 Like

Thanks @colinvwood!

@Epidemiologist_GJC - if you can follow up and let us know if you run into further issues that would be very helpful. We do intend to keep genome-sampler up-to-date, but it's been a while since we've done a new release. If it's not working, we'll figure out what's needed to bring it up-to-date.

Dear Colin,

Many thanks for your prompt response, i tried your solution, but still it didn't work see below:

I really appreciate your help and guidance

Moh Alkhamis

Dear Greg,

I'm a big fan of your genomesampler package, i think it should be integrated within any genomic surviellence systems for infectious disease, see my related work citing your package:

https://academic.oup.com/ve/article/8/1/veac040/6588201

I'm looking forward for new update on your package, thanks for the hard work and support for the community.

Regards

Moh A. Alkhamis

2 Likes

Hi @Epidemiologist_GJC, Thanks so much for the positive feedback and for sharing the link to your paper. It's great to know that it's been useful to others!

Give us a few days and we'll get the environment updated and sorted out, and ideally we'll get genome-sampler added to the new QIIME 2 Library (https://library.qiime2.org) in that time. That will help us ensure that it stays up-to-date and installable.

Greg

2 Likes

Dear Greg,

Thank you so much for your prompt response, and congrats on developing such a useful phylogenetic tool. I will be looking forward to test the new update.

Regards

Moh

1 Like

Hi @Epidemiologist_GJC, Just wanted to follow up to let you know we have updates in progress. It's mostly ready to go but we're fixing up some of the documentation. Should be all set next week, and I'll follow up here to let you know when that's the case.

Dear Greg,

Many thanks for the prompt response and efforts into, looking forward for the new update. Cheers!

Hi @Epidemiologist_GJC, thanks for waiting. We should be good to go now. There is now a 2025.02.0 release of genome-sampler which builds on the QIIME 2 Framework version 2024.10.

The documentation site has also been transitioned to https://genome-sampler.readthedocs.io, and the project is now hosted on the QIIME 2 Library.

I recommend the following command for installing:

conda env create --name genome-sampler-2025.02.0 --file https://raw.githubusercontent.com/caporaso-lab/genome-sampler/refs/heads/dev/environment-files/genome-sampler-qiime2-amplicon-2024.10.yml

(For folks coming across this post in the future, the most recent install instructions should be obtained from here. The instructions at that link are currently correct - just not as user-friendly as I'd like them to be. :fire::fire:)

Happy genome sampling!

1 Like