Unable to install through anaconda

[Angelos-Gk]

Hi everyone, first of all I am on MacOS (Sonoma Version 14.4). I am trying to install cellsnp-lite through anaconda by using the suggested command:

conda install -c bioconda cellsnp-lite

However the output that I get is this:

Channels:

• bioconda
• conda-forge
• defaults
  Platform: osx-arm64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

• cellsnp-lite

Current channels:

• https://conda.anaconda.org/bioconda
• https://conda.anaconda.org/conda-forge
• defaults

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

I have tried updating anaconda or creating new environments but it still produces the same error.
Also when I try to search for the package:
conda search cellsnp-lite
Loading channels: done
No match found for: cellsnp-lite. Search: cellsnp-lite

My question is, has the package been retracted from anaconda/bioconda?

[Sharm8]

I'm having the same issue on a linux HPC.

[hxj5]

Hi, searching and installing cellsnp-lite work well on my Linux HPC. Can you try installing again? or you may report the issue to bioconda.

FYI, my conda version is 4.12.0 (with anaconda3). The conda channels are (conda config --show channels):

channels:
  - conda-forge
  - bioconda
  - defaults

[Sharm8]

Hi! It worked for me when I set "conda config --set channel_priority flexible" as I had it set to "strict" before. Thank you for your help!

[Angelos-Gk]

Update:
I completely uninstalled anaconda and installed miniconda instead. I still get the package not found error. When i run the "conda search" command, in order to get a list of all the installable packages (installable not installed) cellsnp-lite does not appear on the list. For some reason, other bioconda/conda-forge packages appear, but not this specific one. Does anybody have any solutions to this? I tried compiling from source but I get an error during the compiling, which I think it has to do with the architecture of my system os-arm64. Any ideas? (ideally i would like to manage to install through conda)

[hxj5]

Hi, it seems bioconda does not compile packages for osx-arm64 platform, according to this conda issue (Feb, 2022). You may try setting up an osx-64 (intel) conda env and then installing cellsnp-lite on your ARM Mac, as suggested in the stackoverflow threads conda package not found ... and How to set up a conda osx-64 environment on ARM mac?.

[Angelos-Gk]

Thank you very much!! As it seems, the different architecture was the issue. As soon as I tried creating a new environment and specifying a different architecture, the issue was resolved and I was able to install cellsnp-lite.

[kevinrue]

Hi, searching and installing cellsnp-lite work well on my Linux HPC. Can you try installing again? or you may report the issue to bioconda.

FYI, my conda version is 4.12.0 (with anaconda3). The conda channels are (conda config --show channels):

channels:
  - conda-forge
  - bioconda
  - defaults

Had the same issue, and listing conda-forge before bioconda did the trick for me!

My conda yaml:

name: cellsnp_lite
channels:
  - conda-forge # note the importance listing conda-forge first
  - bioconda
  - defaults
dependencies:
  - cellsnp-lite

[roshni-b]

Also had the architecture issue, am on osx-arm, configured the conda env for os-x with conda config --env --set subdir osx-64 and it then worked fine.