PackagesNotFoundError unable to install snp-sites and snippy via bioconda

[gloriajzhou]

I would like to install snippy via bioconda using the command: conda install -c bioconda snippy

However, I receive the following error:

Channels:

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

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides snp-sites >=2.4 needed by snippy-4.4.0-0

Could not solve for environment specs The following package could not be installed └─ snippy =* * is not installable because it requires └─ snp-sites >=2.4 *, which does not exist (perhaps a missing channel).

Next, I tried to install snp-sites via bioconda using: conda install -c bioconda snp-sites

However, I then received this error:

Channels:

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

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

• snp-sites

Current channels:

• https://conda.anaconda.org/bioconda
• defaults
• https://conda.anaconda.org/r
• https://conda.anaconda.org/conda-forge
• https://repo.anaconda.com/pkgs/main
• https://repo.anaconda.com/pkgs/r

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.

Any advice to resolve this issue would be greatly appreciated.

[Wytamma]

Hi @gloriajzhou,

This might be related to osx-arm64 to Can you try installing snippy 4.6.0?

Here's notebook with installation on linux -> https://colab.research.google.com/drive/1yOu6BbPsFlkdRydJNZ80xhi54YwDMzun?usp=sharing

[yaotianran]

Perhaps you need an extra channel: anaconda

channels:
  - defaults
  - bioconda
  - anaconda
  - conda-forge
  - r

This works for me. Besides Snippy needs so many dependencies that it should be installed in a separated environment.

conda create --name snippy -c bioconda snippy

Nonetheless the conda version has a bug that the bcftools installed with Snippy fails to run. A work around is to replace "/envs/snippy/bin/bcftools" with a static binary version of bcftools.