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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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snakePipes createEnvs fails #1016

Open musikutiv opened 5 months ago

musikutiv commented 5 months ago

after performing installation steps as provided in docs

conda install mamba -c conda-forge && mamba create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes

snakePipes createEnvs fails with Creating environment from /work/project/becvil_004/miniconda3/envs/snakePipes/lib/python3.12/site-packages/snakePipes/shared/rules/envs/shared.yaml in /work/project/becvil_004/package/mamba/envs usage: mamba [-h] command ... mamba: error: unrecognized arguments: --force There was an error when creating the environments!

any clues how I can solve the problem?

cluster running CentOS, mamba 1.5.7, conda 24.5.0

WardDeb commented 5 months ago

This is fixed in the develop branch, but not released yet. As a workaround you can pip install from develop. Do note you probably need to cap pulp as well (#991).