ModuleNotFoundError: No module named 'cutadapt.cli'

[Chloelyc]

Hi,

I'm trying to install cutadapt using pip in a virtual environment using the following command:

virtualenv cutadapt-venv pip install cutadapt

I'm working on a server so I can't access the root. My python version is Python 3.11.3 and the cutadapt version is 4.5.

I encountered the error when I tried to use trimgalore:

Traceback (most recent call last): line 5, in from cutadapt.cli import main_cli ModuleNotFoundError: No module named 'cutadapt.cli' Failed to execute Cutadapt properly. Please install Cutadapt first and make sure it is in the PATH, or specify the path to the Cutadapt executable using --path_to_cutadapt /path/to/cutadapt

The content of cutadapt was:

import re import sys from cutadapt.cli import main_cli if name == 'main': sys.argv[0] = re.sub(r'(-script.pyw|.exe)?$', '', sys.argv[0]) sys.exit(main_cli())

And there was no cutadapt.cli that I could import from, which I assumed was the problem. I have tried reinstalling cutadapt but it did not work. Do you know how I can fix this issue? Thanks so much!

[marcelm]

Hi, maybe you did not activate the virtual environment after creating it?

The full list of commands to install cutadapt using a virtual environment is:

virtualenv cutadapt-venv
source cutadapt-venv/bin/activate
pip install cutadapt

You also need to remember to activate the virtual environment (the source ... step above) every time you open a new shell and want to run cutadapt.

Another option is to install Cutadapt with pipx. This is much easier, but only if you already have pipx installed. Try this: pipx install cutadapt Then you don’t need the activation step, pipx takes care of that for you.