mamba 2.0.0 doesn't support the --no-default-packages option #3108
Description
Snakemake version
8.20.5
Describe the bug
When using a fresh Conda environment with Mamba and Snakemake as currently provided by Conda-forge and bioconda, the --use-conda option to Snakemake breaks—Snakemake is unable to instantiate new Conda environments, and no workflows will run that do not already have environments instantiated.
This is because Mamba 2.0.0, released last week, no longer supports the --no-default-packages option that Snakemake passes when creating an environment.
Logs
Assuming unrestricted shared filesystem usage.
host: […]
Building DAG of jobs...
Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Creating conda environment […]...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /Users/[…]:
Command:
mamba env create --quiet --no-default-packages --file "/Users/[…]/.snakemake/conda/c45282c236d9f5a6037ec06524bdd8ef_.yaml" --prefix "/Users/[…]/.snakemake/conda/c45282c236d9f5a6037ec06524bdd8ef_"
Output:
The following argument was not expected: --no-default-packages
Run with --help for more information.
Minimal example
Pick your favourite workflow that uses conda environments, and:
conda create -n snakemake_mamba_test -c conda-forge mamba
conda activate snakemake_mamba_test
conda install -c bioconda snakemake
snakemake --use-conda --cores 1Additional context
N/A