Erreur installation de snakemake/nextflow avec mamba
L'activation de conda base
interfère avec le client slipstream
.
install.sh
# Install snakemake nextflow
echo "Install SnakeMake, Nextflow (with Conda/Mamba)"
conda activate base
${MAMBA_BIN} create -y -c conda-forge -c bioconda -n nextflow nextflow
${MAMBA_BIN} create -y -c conda-forge -c bioconda -n snakemake snakemake
conda deactivate
/var/log/slipstream/client/machine.slipstream.log
Using mamba.
Install SnakeMake, Nextflow (with Conda/Mamba)
Traceback (most recent call last):
File "/var/lib/miniforge/bin/mamba", line 7, in <module>
from mamba.mamba import main
File "/var/lib/miniforge/lib/pypy3.9/site-packages/mamba/mamba.py", line 16, in <module>
from conda.cli.common import check_non_admin, confirm_yn, specs_from_url
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/cli/common.py", line 16, in <module>
from ..exceptions import (
File "/var/lib/miniforge/lib/pypy3.9/site-packages/conda/exceptions.py", line 16, in <module>
from requests.exceptions import JSONDecodeError
ImportError: cannot import name 'JSONDecodeError' from 'requests.exceptions' (/opt/slipstream/client/lib/requests/exceptions.py)