marvel ModuleNotFoundError: No module named 'sklearn.ensemble.forest'

papanikos / MARVEL

MARVEL: Metagenomic Analyses and Retrieval of Viral ELements

GNU General Public License v3.0

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Open papanikos opened 3 years ago

papanikos commented 3 years ago

According to this, with newer versions of scikit-learn the forest module has been renamed to sklearn.ensemble._forest.

So, create a fresh environment with

$ conda create -n marvel hmmer prokka numpy scipy biopython=1.75 scikit-learn=0.21.3

Same goes for biopython, I was getting some AlignIO related error. Once rolling back to 1.75 it was fixed.

papanikos commented 3 years ago

Include the full env specs in the repo, before closing

papanikos commented 3 years ago

Both this and #1 have been addressed on branch fix_1 .
A PR to the original repo is also now open at [https://github.com/LaboratorioBioinformatica/MARVEL/pull/6]() .
Giving it some time to see if there is any chance of getting it merged upstream.

For now

git clone https://github.com/papanikos/MARVEL -b fix_1

will clone the repo and checkout the branch with the fix for #1 and the environment.yml