Fix picrust2-env.yaml dependencies#378
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R-Wright-1 merged 1 commit intopicrust:masterfrom Mar 4, 2025
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1. ete3 has to be installed from etetoolkit channel. conda-forge does not work, even though it is listed on https://anaconda.org/conda-forge/ete3. 2. Installing sepp 4.5.5 requires python3.10. 3. Runnning test requires typeguard 4.4.2 to be specified separately.
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Thanks so much for catching these and adding this! |
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When I install PICRUSt2-2.6.0 from this source wget https://github.com/picrust/picrust2/archive/v2.6.0.tar.gz, I receive one failure when I run pytest. It fails at tests/test_place_seqs.py. All 60 other tests pass. platform linux -- Python 3.10.16, pytest-8.3.5, pluggy-1.5.0 |
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I am seeing the same error in pytest but I don't have a solution for it, This seems to be relevant with sepp 4.5.5 and how it uses pplacer internally. smirarab/sepp#121 might be helpful. Briefly it says the pplacer bundled with sepp produces segfault while newer pplacer version outputs slightly different table, which sepp cannot parse. |
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Current dependencies specified in picrust2-env.yaml does not install using mamba/conda env create -f picrust2-env.yaml. These changes need to be made for successful installment.
The updated package has been tested with pytest under source directory.
I sincerely appreciate the efforts of the developers to maintain this wonderful package and expand its functionality continously. It's such a blessing for the microbial bioinformatics community to have it🤗