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Failure of installing pybedtools and rpy2 #70

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LiuCanidk opened this issue Nov 7, 2024 · 1 comment
Open

Failure of installing pybedtools and rpy2 #70

LiuCanidk opened this issue Nov 7, 2024 · 1 comment

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@LiuCanidk
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LiuCanidk commented Nov 7, 2024

Thanks for developing this nice tool
After running these commands:
mamba create -n SComatic -y python=3.7 r-base=3.6.1 samtools datamash bedtools
mamba activate SComatic
pip install -r requirements.txt
I encountered an error about building wheels on the requirements of SComatic: pybedtools and rpy2:
image
image

I followed the instruction of creating a new conda environment with exactly the code provided in the github page, but found this error. Could you please tell me why this occur and how should I do to install SComatic properly?

I then tried install rpy2=2.9.4 via conda, it works but still cannot install pybedtools

Any advice or suggestions would be greatly appreciated! Thanks in advance

@LiuCanidk
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conda install -y bioconda::pybedtools works for me but upgrade many dependent packages. E.g., rpy2 change to >3.0
It seems to be associated with old version of setuptools with old version of python 3.7 in the requirements.

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