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@nylander
Last active April 5, 2022 08:08
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Fix error in python for installing nf-core on Ubuntu 20.04, python 3.8
Recently, I tried to upgrade [nf-core](https://nf-co.re/) on my Ubuntu Linux but the execution after installation failed with errors from a python module.
Upgrading the python library ["rich"](https://rich.readthedocs.io/en/stable/introduction.html) solved the issue.
Steps below:
```
$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=20.04
DISTRIB_CODENAME=focal
DISTRIB_DESCRIPTION="Ubuntu 20.04.4 LTS"
$ python -V
Python 3.8.10
$ pip3 -V
pip 20.0.2 from /usr/lib/python3/dist-packages/pip (python 3.8)
$ pip3 install nf-core
$ nf-core --version
Traceback (most recent call last):
File "/home/nylander/.local/bin/nf-core", line 5, in <module>
from nf_core.__main__ import run_nf_core
File "/home/nylander/.local/lib/python3.8/site-packages/nf_core/__main__.py", line 20, in <module>
import nf_core.lint
File "/home/nylander/.local/lib/python3.8/site-packages/nf_core/lint/__init__.py", line 21, in <module>
import nf_core.modules.lint
File "/home/nylander/.local/lib/python3.8/site-packages/nf_core/modules/__init__.py", line 11, in <module>
from .info import ModuleInfo
File "/home/nylander/.local/lib/python3.8/site-packages/nf_core/modules/info.py", line 9, in <module>
from rich.console import Group
ImportError: cannot import name 'Group' from 'rich.console' (/home/nylander/.local/lib/python3.8/site-packages/rich/console.py)
$ pip3 uninstall nf-core
$ pip3 install --upgrade --user rich
$ pip3 show rich
Name: rich
Version: 12.0.1
Summary: Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal
Home-page: https://github.com/willmcgugan/rich
Author: Will McGugan
Author-email: willmcgugan@gmail.com
License: MIT
Location: /home/nylander/.local/lib/python3.8/site-packages
Requires: pygments, commonmark
Required-by: rich-click
$ pip3 install nf-core
$ nf-core --version
```
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