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deeptools / deepTools

Tools to process and analyze deep sequencing data.
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ImportError: cannot import name 'colormaps' #1339

Closed VihanYeh closed 2 hours ago

VihanYeh commented 1 day ago

The deeptools work well till I update the samtools. I already tried update via conda. There is the error message: Traceback (most recent call last): File "/Users/lab/miniconda3/envs/bioinfo/bin/bamCompare", line 7, in from deeptools.bamCompare import main File "/Users/lab/miniconda3/envs/bioinfo/lib/python3.6/site-packages/deeptools/bamCompare.py", line 9, in from deeptools import writeBedGraph File "/Users/lab/miniconda3/envs/bioinfo/lib/python3.6/site-packages/deeptools/writeBedGraph.py", line 9, in from deeptools.utilities import getCommonChrNames File "/Users/lab/miniconda3/envs/bioinfo/lib/python3.6/site-packages/deeptools/utilities.py", line 7, in from deeptools import cm # noqa: F401 File "/Users/lab/miniconda3/envs/bioinfo/lib/python3.6/site-packages/deeptools/cm.py", line 33, in from matplotlib import colors, colormaps as mpl_cm ImportError: cannot import name 'colormaps'

WardDeb commented 19 hours ago

My guess is your matplotlib version is too old. Please try to re-install deeptools in a new conda env (py 3.6 is no longer supported).

VihanYeh commented 2 hours ago

Thank you. I update to Python 3.10, and the deeptools works now.