Issue installing AMPtk (Mac OS - M1 chip)

[cpbivins28]

Hi,

I'm currently unable to successfully install AMPtk.

Following the installation instructions on https://amptk.readthedocs.io/en/latest/ - I type in the first three commands:

conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge

No problems here - everything seems to be fine.

Then I run:

conda create -n amptk amptk

And I get this:

Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

And that's it. My computer is not actually telling me what the unsatisfiable error is. I then tried running the following:

conda install -c conda-forge amptk

And get this:

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

At least now it's telling me that there are some incompatibilities, but again the computer does not actually list what the incompatibilities are.

I would greatly appreciate anyone's help with this!

-C

[nicolereynolds2]

Hi,

I am also using a Mac M1. I don't have an answer (I ran into the same problem when trying to install using conda), but I was able to install amptk using the GitHub repository instructions

#clone the repository git clone https://github.com/nextgenusfs/amptk.git

#then install, optional add --prefix to control location python setup.py install --prefix /User/Tools/amptk

Another option I came across is setting up an alternate version of terminal that operates through Rosetta (that can help get around the ARM incompatibility issues) e.g. https://taylorreiter.github.io/2022-04-05-Managing-multiple-architecture-specific-installations-of-conda-on-apple-M1/

Amptk has been working so far after using the github instructions on the native terminal (after also installing a lot of the dependencies separately).

hope that helps!

UPDATE Amptk was working after using the github instructions on the native terminal until I tried to assign taxonomy. Then I kept getting an error about MAFFT/FastTree (even though I installed MAFFT), but unfortunately I didn't save the specific error text. I tried a number of different ways to fix this, but I couldn't get it to work.

Then I went back to the idea of using Rosetta. I used these commands

CONDA_SUBDIR=osx-64 conda create -n rosetta python   # create a new environment called rosetta with intel packages.
conda activate rosetta
python -c "import platform;print(platform.machine())"
conda config --env --set subdir osx-64  # make sure that conda commands in this environment use intel packages

from https://github.com/conda-forge/miniforge/issues/165#issuecomment-860233092 then used the conda commands to install amptk and make an environment.

#setup your conda env with bioconda, type the following in order to setup channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

#create amptk env (optional)
conda create -n amptk amptk

Now I have been able to complete all processing steps in amptk (pre-processing through taxonomy assignment)

[seqing-answers]

Did you ever find a work-around for this issue? I am currently running into this problem on my M2 Macbook pro.