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picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
GNU General Public License v3.0
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Installing problem into MacBook Air m1 terminal #331

Closed kumarrupin closed 3 months ago

kumarrupin commented 1 year ago

I have tried from both bioconda and from source both way are not working for me Screenshot 2023-11-09 at 11.39.20 AM.pdf Screenshot 2023-11-09 at 12.19.02 PM.pdf

kumarrupin commented 1 year ago

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:

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:

R-Wright-1 commented 11 months ago

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 commented 11 months ago

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 commented 11 months ago

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 commented 11 months ago

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 commented 11 months ago

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 commented 10 months ago

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 commented 7 months ago

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 commented 3 months ago

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