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Install picrust2 to save: pkg_resources.DistributionNotFound: The 'cython' distribution was not found and is required by biom-format

Installation method:

All installation instructions are in more detail here.

First, clone the repository and enter the directory:

Git clone https://github.com/picrust/picrust2.gitcd

Next, install the required dependencies listed here.

Install PICRUSt2 into it's own environment using conda:

Conda env create-f picrust2-env.yamlsource activate picrust2pip install-- no-deps-- editable.

Finally, run the tests to verify the install was successful:

Pytest

Test error:

Standard error of the above failed command:

Traceback (most recent call last):

File "/ share/work/biosoft/conda/Miniconda3.8/envs/picrust2/bin/picrust2_pipeline.py", line 4, in

_ _ import__ ('pkg_resources'). Require (' PICRUSt2==2.3.0b0')

File "/ share/work/biosoft/conda/Miniconda3.8/envs/picrust2/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3267, in

@ _ call_aside

File "/ share/work/biosoft/conda/Miniconda3.8/envs/picrust2/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3251, in _ call_aside

F (* args, * * kwargs)

File "/ share/work/biosoft/conda/Miniconda3.8/envs/picrust2/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3280, in _ initialize_master_working_set

Working_set = WorkingSet._build_master ()

File "/ share/work/biosoft/conda/Miniconda3.8/envs/picrust2/lib/python3.6/site-packages/pkg_resources/__init__.py", line 582, in _ build_master

Ws.require (_ _ requires__)

File "/ share/work/biosoft/conda/Miniconda3.8/envs/picrust2/lib/python3.6/site-packages/pkg_resources/__init__.py", line 899, in require

Needed = self.resolve (parse_requirements (requirements))

File "/ share/work/biosoft/conda/Miniconda3.8/envs/picrust2/lib/python3.6/site-packages/pkg_resources/__init__.py", line 785, in resolve

Raise DistributionNotFound (req, requirers)

Pkg_resources.DistributionNotFound: The 'cython' distribution was not found and is required by biom-format

Solution:

Reinstall: pip install biom-format

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