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aineniamh / squirrel

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ImportError: cannot import name 'DYNAMIC_FILL' from 'snakemake.common' #5

Closed BrightMAK closed 2 months ago

BrightMAK commented 10 months ago

Hi, I got this error message after installation. Any advice on how to get this fixed?

Traceback (most recent call last): File "/home/bmak/anaconda3/envs/squirrel/bin/squirrel", line 5, in from squirrel.command import main File "/home/bmak/anaconda3/envs/squirrel/lib/python3.12/site-packages/squirrel/command.py", line 4, in import squirrel.utils.custom_logger as custom_logger File "/home/bmak/anaconda3/envs/squirrel/lib/python3.12/site-packages/squirrel/utils/custom_logger.py", line 23, in from snakemake.common import DYNAMIC_FILL ImportError: cannot import name 'DYNAMIC_FILL' from 'snakemake.common' (/home/bmak/anaconda3/envs/squirrel/lib/python3.12/site-packages/snakemake/common/init.py)

aineniamh commented 10 months ago

Hi @BrightMAK, this seems like a version incompatibility with whatever snakemake version you installed. I've just pushed a change that will pin a specific snakemake version.

To rectify quickly, I recommend trying: mamba install snakemake-minimal=7.32 This should solve the error you're currently getting

Alternatively, you can try doing a full update: 1) git pull the latest changes to the repository 2) conda activate squirrel 3) mamba env update -f environment.yml 4) pip install . That should do it

BrightMAK commented 10 months ago

Thanks for the prompt response, @aineniamh. The problem is resolved.