Issues installing AMR finder plus package

[Charlotteabbey3]

I have been trying to use the wiki page to download AMR finder on terminal on mac but this error keeps popping up both trying to use homebrew and conda. Any advice would be great :)
(base) u2252732@11-G3-029195-22 amr-master % source ~/miniconda3/bin/activate
(base) u2252732@11-G3-029195-22 amr-master % conda create -y -c conda-forge -c bioconda -n amrfinder --strict-channel-priority ncbi-amrfinderplus
Channels:

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

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

• ncbi-amrfinderplus

Current channels:

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

[evolarjun]

Hi @Charlotteabbey3,

Sorry you ran into this issue. The problem for bioconda is that the blast package that ncbi-amrfinderplus depends on is not available for osx-arm64. We don't control that package and for some reason it hasn't been updated to run on osx-arm64.

AMRFinderPlus itself builds and runs find on OSX, in fact I have an ARM Mac terminal myself and use it there. I didn't know there was a homebrew package for AMRFinderPlus, so I haven't tried it and I'm not sure what the issue with it is.

If you have the Apple Developer Tools (free) downloaded and installed you should be able to compile the dependencies and install AMRFinderPlus yourself fairly easily.

Homebrew does have HMMER and BLAST packages, and I think libcurl comes on MacOS by dfault so you should be able to get the dependencies for AMRFinderPlus with the following:

To install Homebrew:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

To install HMMER and BLAST:

 brew install blast
 brew install hmmer

Download the source code and compile AMRFinderPlus

git clone https://github.com/ncbi/amr.git
cd amr
git submodule update --init --recursive
make -j

Download the database and test the version you just built

./amrfinder -u
make test

You can then use the AMRFinderPlus in the amr/ directory you just created or you can install it centrally. See https://github.com/ncbi/amr/wiki/Compile-from-source for more details.

Let us know that doesn't work for you.

Arjun