下载 blat 到 M1 mac

Question

I am trying to download the blat package so that I can use the GAMMA program to analyze mutations in some sequences. I have bioconda install and I am using one-liner code to download blat described here: https://shanguangyu.com/articles/install-blat-on-mac-with-one-liner-command/

I think the issue could be that blat is not made for M1 macs. I previously had it installed on an older mac but I don't remember how I did that. I am a beginner/proficient coder so it could be an obvious error. Any help is appreciated.

Here is my code:

conda install -c bioconda blat

Here is my error:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

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

  - blat

Current channels:

  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch

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

    https://anaconda.org

Answer 1

You got to the root of the issue. M1 Macs use an ARM64-based architecture as opposed to x64. The website for blat does not list ARM compatibility, and, addressing the M1 specifically, a quick examination of the last update to the files shows that they predate the launch of the Apple Silicon Macs, just like the website you got the command from . Anaconda itself added support for ARM64 only recently . x64 translation does exist for macOS apps, but I don't think I've heard of one for blat.

Answer 2

From post update

This seems to be a common issue for Python users on new M1 macs. Many python packages are not made for ARM chips

This is solved by downloading homebrew and miniforge and using this code:

CONDA_SUBDIR=osx-64 conda create -n [environment]   # create a new environment
conda activate [environment]
conda env config vars set CONDA_SUBDIR=osx-64  # subsequent commands use intel packages

https://naolin.medium.com/conda-on-m1-mac-with-miniforge-bbc4e3924f2b https://towardsdatascience.com/using-conda-on-an-m1-mac-b2df5608a141 https://github.com/Haydnspass/miniforge#rosetta-on-mac-with-apple-silicon-hardware