Installing problem into MacBook Air m1 terminal about picrust2

[kumarrupin]

This error come while installing from bioconda

(base) rupin@RUPINs-MacBook-Air ~ % conda create -n picrust2 -6 bioconda - conda-forge picrust2=2.5.2
[Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying 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
PackagesNotFoundError: The following packages are not available from current channels:

• hmmer[version='>=3.1b2, ≤3.2.1'1
  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
  https://repo.anaconda.com/pkgs/main/osx-arm64
  https://repo.anaconda.com/pkgs/main/noarch
  https://repo.anaconda.com/pkgs/r/osx-arm64
  https://repo.anaconda.com/pkgs/r/noarch
  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.
  (base) rupin@RUPINs-MacBook-Air ~

this error comes while installing from source

(base) rupin@RUPINs-MacBook-Air picrust2-2.5.2 % conda env create -f picrust2-envyam]
conda activate picrust2 pip install -editable •
Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:

• biom-format[version='>=2.1.10' ]
• r-castor[version='>=1.7.2']
• epa-ng=0.3.8
• gappa=0.8.0
• hmmer[ version='>=3.1b2, <=3.2.1']
• sepp=4.3.10
  Focan ast a tEsoverable environments water com into ens?.
  You can list all discoverable environments with
  Obtaining file:///Users/rupin/picrust2-2.5.2
  Preparing metadata (setup. py) ... done
  Requirement already satisfied: numpy in /Users/rupin/miniconda3/lib/python3.11/site-packages (from PICRUSt2==2.5.2) (1.26.1)
  Requirement already satisfied: h5py in /Users/rupin/miniconda3/lib/python3.11/site-packages (from PICRUSt2==2.5.2) (3.10.0)
  Requirement already satisfied: joblib in /Users/rupin/miniconda3/lib/python3.11/site-packages (from PICRUSt2==2.5.2) (1.3.2)
  Requirement already satisfied: biom-format in /Users/rupin/miniconda3/lib/python3.11/site-packages (from PICRUSt2==2.5.2) (2.1.15)
  Requirement already satisfied: click in /Users/rupin/miniconda3/lib/python3.11/site-packages (from biom-format=>PICRUSt2==2.5.2) (8.1.7)
  Requirement already satisfied: scipy>=1.3.1 in /Users/rupin/miniconda3/lib/python3.11/site-packages (from biom-format->PICRUSt2==2.5.2) (1.11.3)
  Requirement already satisfied: pandas>=0.20.0 in /Users/rupin/miniconda3/lib/python3.11/site-packages (from biom-format->PICRUSt2==2.5.2) (2.1.2)
  Requirement already satisfied: python-dateutil>=2.8.2 in /Users/rupin/miniconda3/lib/python3.11/site-packages (from pandas>=0.20.0->biom-format->PICRUSt2==2.5.2) (2.8.2)
  Requirement already satisfied: pytz>=2020.1 in /Users/rupin/miniconda3/lib/python3.11/site-packages (from pandas>=0.20.0->biom-format->PICRUSt2==2.5.2) (2023.3. post1)
  Requirement already satisfied: tzdata>=2022.1 in /Users/rupin/miniconda3/lib/python3.11/site-packages (from pandas>=0.20.0->biom-format->PICRUSt2==2.5.2) (2023.3)
  Requirement already satisfied: six>=1.5 in /Users/rupin/miniconda3/lib/python3.11/site-packages (from python-dateuti1>=2.8.2-›pandas>=0.20.0->biom-format->PICRUSt2==2.5.2) (1.16.0)
  Installing collected packages: PICRUSt2
  Attempting uninstall: PICRUSt2
  Found existing installation: PICRUSt2 2.5.2
  Uninstalling PICRUSt2-2.5.2:
  Successfully uninstalled PICRUSt2-2.5.2
  Running setup.py develop for PICRUSt2
  Successfully installed PICRUSt2-2.5.2 (base) rupin@RUPINs-MacBook-Air picrust2-2.5.2

[R-Wright-1]

Hi there, based on your second install from source and screenshot, it says that it is successfully installed. Are you sure that it's not installed?

[kumarrupin]

Hi, but when i am activating it continuously showing -

rupin@RUPINs-MacBook-Air picrust2-2.5.2 % conda activate picrust2

EnvironmentNameNotFound: Could not find conda environment: picrust2
You can list all discoverable environments with conda info --envs.

even not found in conda info-----
rupin@RUPINs-MacBook-Air picrust2-2.5.2 % conda info --envs

conda environments:

base /Users/rupin/miniconda3
qiime2-2023.7 /Users/rupin/miniconda3/envs/qiime2-2023.7
qiime2-amplicon-2023.9 /Users/rupin/miniconda3/envs/qiime2-amplicon-2023.9
qiime2-shotgun-2023.9 /Users/rupin/miniconda3/envs/qiime2-shotgun-2023.9
qiime2-tiny-2023.9 /Users/rupin/miniconda3/envs/qiime2-tiny-2023.9

[kumarrupin]

By this command mamba env create -f picrust2-env.yaml
conda activate picrust2
pip install --editable in between it showing

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).

[blakemycake]

I was having a similar issue installing picrust2 on my macbook M1. I was able to resolve the issue by running my terminal in Rosetta, re-installing microconda, and following the instructions to download from source using the command below instead of the mamba command to create the environment:

CONDA_SUBDIR=osx-64 conda env create -f picrust2-env.yaml

[kumarrupin]

thanks ,it is installed by your command. But after pytest command to test it it showing some file or directory are not found.

screentshot-2.pdf

../miniconda3/envs/picrust2/lib/python3.8/subprocess.py:1720: FileNotFoundError
====================================== short test summary info =======================================
FAILED tests/test_place_seqs.py::place_seqs_tests::test_run_place_seqs_pipeline_sepp - SystemExit: 1
FAILED tests/test_workflow.py::workflow_test::test_full_pipeline_tsv - FileNotFoundError: [Errno 2] No such file or directory: 'place_seqs.py'
FAILED tests/test_workflow.py::workflow_test::test_help_calls - FileNotFoundError: [Errno 2] No such file or directory: 'add_descriptions.py'
FAILED tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script - FileNotFoundError: [Errno 2] No such file or directory: 'picrust2_pipeline.py'
FAILED tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script_per_seq_contrib_strat - FileNotFoundError: [Errno 2] No such file or directory: 'picrust2_pipeline.py'
FAILED tests/test_workflow.py::workflow_test::test_picrust2_pipeline_script_per_seq_contrib_strat_skip_norm - FileNotFoundError: [Errno 2] No such file or directory: 'picrust2_pipeline.py'
============================== 6 failed, 55 passed in 93.27s (0:01:33) ===============================

[blakemycake]

Did you change your terminal so it's running in Rosetta? I think I had the same error when I first tried to install it using the command above. I'm not 100% sure why that happened but I believe uninstalling microconda and reinstalling it when running the terminal in Rosetta fixed the issue. You could also try using miniforge instead of microconda!

[R-Wright-1]

Apologies for my slow response on this. I've added what worked for me in here: #314
Could you see if that works?

[R-Wright-1]

I'm just closing this issue as there hasn't been any further response.