Unable to install Kraken 2 and bracken on my Mac using conda

[chrissy005]

Hello,

While I am able to install bowtie2, KrakenTools and samtools just as it is described in the Nature Protocols paper, I am unable to install Kraken2 and Bracken

I used the following code and get the following output:

$ conda install -c conda-forge -c bioconda kraken2 bracken Channels:

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

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides requested kraken2
• nothing provides kraken needed by bracken-1.0.0-1

Could not solve for environment specs The following packages are incompatible ├─ bracken is not installable because it requires │ └─ kraken, which does not exist (perhaps a missing channel); └─ kraken2 does not exist (perhaps a typo or a missing channel).

Also, do you recommend that I can run the microbiome analysis protocol described in the paper on my MacBook Pro or on a HPC?

[ChillarAnand]

kraken2 doesn't have official arm64 support yet.

However you can use brew to install kraken2 on M1(apple silicon) macs.

$ brew install brewsci/bio/kraken2

More details at https://avilpage.com/2024/07/mastering-kraken2-initial-runs.html

[chrissy005]

Thank you, this works