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安装picrust2 保存:pkg_resources.DistributionNotFound: The 'cython' distribution was not found and is required by biom-format
安装方法:
All installation instructions are in more detail here.
First, clone the repository and enter the directory:
git clone https://github.com/picrust/picrust2.git cd
Next, install the required dependencies listed here.
Install PICRUSt2 into it's own environment using conda:
conda env create -f picrust2-env.yaml source activate picrust2 pip install --no-deps --editable .
Finally, run the tests to verify the install was successful:
pytest
测试报错:
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 <module>
__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 <module>
@_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
解决办法:
重新安装:pip install biom-format
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