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snakePipes createEnvs fails #1016

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musikutiv opened this issue Jun 13, 2024 · 1 comment
Open

snakePipes createEnvs fails #1016

musikutiv opened this issue Jun 13, 2024 · 1 comment

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@musikutiv
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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
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WardDeb commented Jun 13, 2024

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).

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