I'm new in the field, so sorry for possible silly mistakes. I'm working with snakemake, so I created a conda environment following their directions:
conda install -c conda-forge mamba
mamba create -c conda-forge -c bioconda -n snakemake snakemake
However, while I was running the basic tutorial (enter link description here) a ModuleNotFoundError occurred:
snakemake --cores 1
ModuleNotFoundError: No module named 'matplotlib'
For this reason, I've installed matplotlib with conda-forge:
conda install -c conda-forge matplotlib
However, when I re-runned the tutorial, I got an ImportError:
ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/init.py) So I decided to install in the same conda environment also pillow:
conda install -c conda-forge pillow
But I obtain the same error running the tutorial.
All of the imported packages are coming from my conda environment:
anaconda3/envs/snakemake/lib/python3.9/site-packages
Besides the path of PIL/pillow which is imported from:
usr/lib/python3/dist-packages
I also update conda, anaconda and all of the packages present in my snakemake environment. Moreover, I checked the presence of PIL with conda list and it is actualy present in my snakemake environment with the same path of other packages (anaconda3/envs/snakemake/lib/python3.9/site-packages).
I've noticed that in other issues it is suggested to uninstall and re install Pillow. Howeever, when I try to uninstall:
pip uninstall Pillow
and
pip3 uninstall Pillow
I obtain:
PermissionError: [Errno 13] Permesso negato: 'BlpImagePlugin.cpython-38.pyc'
Therefore I've tried to force the upgrade:
pip install -U Pillow --user
and
pip3 install -U Pillow --user
And the terminal states that I have succesfully installed Pillow 8.0.1. However, when I import matplotlib the same error occurs:
ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/init.py)
I'm grateful for any hints Thank you
