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MD-Anderson-Bioinformatics / BatchEffectsPackage

The MBatch R package and Docker image are designed to help assess and correct for batch effects.
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Mbatch Python package missing #9

Open jonssonlab opened 9 months ago

jonssonlab commented 9 months ago

Hello, we are trying to download the mbatch python package but there seem to be a setup.py file. Any help is appreciated!

ERROR: mbatch from git+https://github.com/MD-Anderson-Bioinformatics/BatchEffectsPackage.git#egg=mbatch does not appear to be a Python project: neither 'setup.py' nor 'pyproject.toml' found.

TDCasasent commented 9 months ago

I'm not 100% sure of what you are attempting or which part of the docs you are looking at, but it looks like you have left out the &subdirectory=apps/PyMBatch from the pip install command.

https://github.com/MD-Anderson-Bioinformatics/BatchEffectsPackage?tab=readme-ov-file#mbatch-python-environment

conda activate gendev
pip install git+https://github.com/MD-Anderson-Bioinformatics/BatchEffectsPackage.git#egg=mbatch&subdirectory=apps/PyMBatch

Also, please be aware we had a new release over the weekend.