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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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can't use hicDetectLoops #810

Open jrw510 opened 2 years ago

jrw510 commented 2 years ago

hello, i used conda to install hicexplorer in a new environment, but i can't use hicDetectLoops or hicHyperoptDetectLoops,

$ hicDetectLoops -h Traceback (most recent call last): File "/data/jerry/software/miniconda3/envs/hicexplorer/bin/hicDetectLoops", line 4, in from hicexplorer.hicDetectLoops import main File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/hicDetectLoops.py", line 22, in from hicexplorer.lib import cnb File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/lib/init.py", line 2, in from .tadClassifier import TADClassifier File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/lib/tadClassifier.py", line 41, in from cleanlab.classification import LearningWithNoisyLabels ImportError: cannot import name 'LearningWithNoisyLabels' from 'cleanlab.classification' (/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/cleanlab/classification.py)

$ hicHyperoptDetectLoops -h Traceback (most recent call last): File "/data/jerry/software/miniconda3/envs/hicexplorer/bin/hicHyperoptDetectLoops", line 4, in from hicexplorer.hicHyperoptDetectLoops import main File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/hicHyperoptDetectLoops.py", line 11, in from hicexplorer import hicDetectLoops File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/hicDetectLoops.py", line 22, in from hicexplorer.lib import cnb File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/lib/init.py", line 2, in from .tadClassifier import TADClassifier File "/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/hicexplorer/lib/tadClassifier.py", line 41, in from cleanlab.classification import LearningWithNoisyLabels ImportError: cannot import name 'LearningWithNoisyLabels' from 'cleanlab.classification' (/data/jerry/software/miniconda3/envs/hicexplorer/lib/python3.9/site-packages/cleanlab/classification.py)

thanks for your help!

jrw510 commented 2 years ago

$ hicexplorer --version hicexplorer 3.7.2 $ python --version Python 3.9.13

joachimwolff commented 2 years ago

Seems that a dependency changed its API. Please try to install HiCExplorer with a fixed version number for this dependency: conda install hicexplorer cleanlab=0.1 -c bioconda -c conda-forge

Best,

Joachim

jrw510 commented 2 years ago

it works. thank you!

sebastian-gregoricchio commented 2 years ago

I had similar issue and I solved installing this exact version of cleanlab in my conda env:

conda install -c conda-forge 'cleanlab=1.0.1=pyhd8ed1ab_0'

Norbittner commented 2 years ago

The same is true when installing HiCExplorer by cloning the repository it's not working with the current version of cleanlab 2.0.0 but when switching to 1.0.1 it's working fine.

tolender commented 2 years ago

Had this same error message but used "conda install hicexplorer cleanlab=0.1 -c bioconda -c conda-forge" as suggested and it worked. Can you update the main page to make it clearer for others?

Thank you so much!