Downloading blat to M1 mac-CodePudding

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

CodePudding user response：

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.

CodePudding user response：

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