picrust2 installation error on mac m2

[Rebecca Brittain]

Greetings,

I am trying to install Picrust2 on a mac m2 and am getting installation errors regarding incompatible packages (perhaps a type or missing channel). 

I've tried installing from bioconda and get this error:

Looking for: ['picrust2=2.5.2']

bioconda/osx-arm64                                 124.0 B @ 154.0 B/s  0.8s

bioconda/noarch                                    @   1.6MB/s  3.1s

conda-forge/osx-arm64                              @   2.1MB/s  4.4s

conda-forge/noarch                                 @   3.2MB/s  4.8s

Could not solve for environment specs

The following package could not be installed

└─ picrust2 2.5.2**  is uninstallable because it requires

   └─ biom-format >=2.1.10 , which does not exist (perhaps a missing channel).

And when I try to install from source, I get this error:

(base) rebeccab@vpn17225160148:~/picrust2-2.5.2$ mamba env create -f picrust2-env.yaml

conda-forge/osx-arm64                                       Using cache

conda-forge/noarch                                          Using cache

bioconda/osx-arm64                                          Using cache

bioconda/noarch                                             Using cache

r/osx-arm64                                        124.0 B @ 176.0 B/s  0.7s

anaconda/noarch                                    462.2kB @ 403.6kB/s  1.2s

r/noarch                                           864.1kB @ 687.3kB/s  1.3s

anaconda/osx-arm64                                   1.0MB @ 744.8kB/s  1.4s

pkgs/main/osx-arm64                                  2.1MB @   1.4MB/s  1.6s

pkgs/main/noarch                                   853.2kB @ 495.1kB/s  1.0s

pkgs/r/osx-arm64                                   118.0 B @  68.0 B/s  0.5s

pkgs/r/noarch                                        2.0MB @ 860.9kB/s  1.2s

Looking for: ["biom-format[version='>=2.1.10']", 'cython', 'epa-ng=0.3.8', 'gappa=0.8.0', "glpk[version='>=4.65']", "h5py[version='>=2.10.0']", "hmmer[version='>=3.1b2,<=3.2.1']", "jinja2[version='>=2.11.3']", "joblib[version='>=1.0.1']", "numpy[version='>=1.19.5']", "pandas[version='>=1.1.5']", "pytest[version='>=4.4.1']", "pytest-cov[version='>=2.6.1']", "python[version='>=3.5,<3.9']", "r-base[version='>=3.5.1']", "r-castor[version='>=1.7.2']", "scipy[version='>=1.2.1']", 'sepp=4.3.10']

Could not solve for environment specs

The following packages are incompatible

├─ biom-format >=2.1.10  does not exist (perhaps a typo or a missing channel);

├─ epa-ng 0.3.8**  does not exist (perhaps a typo or a missing channel);

├─ gappa 0.8.0**  does not exist (perhaps a typo or a missing channel);

├─ hmmer >=3.1b2,<=3.2.1  does not exist (perhaps a typo or a missing channel);

├─ r-castor >=1.7.2  does not exist (perhaps a typo or a missing channel);

└─ sepp 4.3.10**  does not exist (perhaps a typo or a missing channel).

Any seasoned advice for a newbie would be greatly appreciated!

best,

Rebecca

[Eduardo Castro]

Hi all,

I have the exact same problem in a Mac m1 ultra. I should add that I do have biom-format installed and in the path, though it doesn't seem to help.

Cheers,

Eduardo

System information

==================

         Platform:    darwin

   Python version:    3.11.6 | packaged by conda-forge | (main, Oct  3 2023, 10:37:07) [Clang 15.0.7 ]

Python executable:    /Users/harrison/miniconda3/bin/python

Dependency versions

===================

click version:    8.1.7

NumPy version:    1.26.1

SciPy version:    1.11.3

 h5py version:    3.10.0

biom-format package information

===============================

biom-format version:    2.1.15

[Rebecca Brittain]

Hi Eduardo,

I was not able to resolve this on my mac but I was able to resolve it on our university hpc (which was giving me the same errors). Not sure if you have access to one, but basically I did the following:

1- did a fresh install of miniconda3

2- added bioconda channels and changed the order

# add bioconda channels: https://bioconda.github.io/recipes/picrust2/README.html & https://www.ddocent.com//bioconda/

conda config --add channels defaults

conda config --add channels bioconda

conda config --add channels conda-forge

# order matters, check:

conda config --show channels

channels:

  - conda-forge

  - bioconda

  - defaults

# change channel order: https://bioconda.github.io/tutorials/gcb2020.html#conda-channels

conda config --prepend channels bioconda

conda config --prepend channels conda-forge

3- installed picrust2 from source (stand alone)

I'm not sure how helpful this will be for you (or others)- I hope you get this resolved!

Best,

Rebecca