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I have installed nf-core and Nextflow using Micromamba. The installation was successful, but when I run the nf-core command, I receive the following error:
Traceback (most recent call last):
File "/Users/kojix2/miniconda3/envs/nextflow/bin/nf-core", line 7, in <module>
from nf_core.__main__ import run_nf_core
File "/Users/kojix2/miniconda3/envs/nextflow/lib/python3.12/site-packages/nf_core/__main__.py", line 19, in <module>
import nf_core.lint
File "/Users/kojix2/miniconda3/envs/nextflow/lib/python3.12/site-packages/nf_core/lint/__init__.py", line 22, in <module>
import nf_core.modules.lint
File "/Users/kojix2/miniconda3/envs/nextflow/lib/python3.12/site-packages/nf_core/modules/__init__.py", line 12, in <module>
from .mulled import MulledImageNameGenerator
File "/Users/kojix2/miniconda3/envs/nextflow/lib/python3.12/site-packages/nf_core/modules/mulled.py", line 10, in <module>
from galaxy.tool_util.deps.mulled.util import build_target, v2_image_name
File "/Users/kojix2/miniconda3/envs/nextflow/lib/python3.12/site-packages/galaxy/tool_util/deps/__init__.py", line 10, in <module>
from galaxy.util import (
File "/Users/kojix2/miniconda3/envs/nextflow/lib/python3.12/site-packages/galaxy/util/__init__.py", line 74, in <module>
from .path import safe_contains, safe_makedirs, safe_relpath # noqa: F401
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kojix2/miniconda3/envs/nextflow/lib/python3.12/site-packages/galaxy/util/path/__init__.py", line 5, in <module>
import imp
ModuleNotFoundError: No module named 'imp'
I believe this issue is related to the removal of the imp module in Python 3.12. While this seems to be a Galaxy-related issue and not directly caused by nf-core, I wanted to report it here for reference, as the error still occurs even after following the installation steps in the README.
In my case, the simplest solution was to downgrade to Python 3.11:
Hi @kojix2, looks like you are using an old version of nf-core, the current stable version is 2.14.1. I recommend installing the latest version where you shouldn't see this error.
Thank you, I have updated nf-core to the latest version and this error no longer occurs. The reason why the latest nf-core could not be installed automatically is that the version of pytest-workflow was out of date. bioconda has a higher priority than conda-forge and the pytest-workflow registered in bioconda was out of date.
Description of the bug
Hello,
I have installed nf-core and Nextflow using Micromamba. The installation was successful, but when I run the
nf-core
command, I receive the following error:I believe this issue is related to the removal of the
imp
module in Python 3.12. While this seems to be a Galaxy-related issue and not directly caused by nf-core, I wanted to report it here for reference, as the error still occurs even after following the installation steps in the README.In my case, the simplest solution was to downgrade to Python 3.11:
Thank you!
Command used and terminal output
System information
Apple M2 macOS Sonoma 14.6.1
micromamba 1.5.9
nextflow version 24.04.4.5917
nf-core, version 2.4.1
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