I have cloned galaxy into my ubuntu machine and when I did sh run.sh this is what I get
Traceback (most recent call last):
File “”, line 1, in
File “/home/aj/Usegalaxy/galaxy/lib/galaxy/util/init.py”, line 54, in
import requests
ModuleNotFoundError: No module named ‘requests’
Anything Iam missing or getting wrong ?
Welcome, @ajreddys
Below are the resources we have for setting up a local Galaxy.
The Docker might be a better choice if you don’t want or need to invest in the customized server administration tasks.
requests is a dependency of Galaxy that should have been installed automatically during startup. What is the output of python --version command on your system? Also the full output of the Galaxy startup output would be helpful.
Usegalaxy/galaxy$ sh run.sh
Activating virtualenv at .venv
Requirement already satisfied: pip>=20.3 in ./.venv/lib/python3.12/site-packages (24.0)
Requirement already satisfied: wheel in ./.venv/lib/python3.12/site-packages (0.43.0)
Looking in indexes: Package Index, Simple index
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Ignoring whoosh: markers ‘python_version >= “3.7” and python_version < “3.12”’ don’t match your environment
Ignoring wrapt: markers ‘python_version >= “3.7” and python_version < “3.12”’ don’t match your environment
Ignoring yacman: markers ‘python_version >= “3.7” and python_version < “3.12”’ don’t match your environment
Ignoring yarl: markers ‘python_version >= “3.7” and python_version < “3.12”’ don’t match your environment
Ignoring zipp: markers ‘python_version >= “3.7” and python_version < “3.12”’ don’t match your environment
Ignoring zipstream-new: markers ‘python_version >= “3.7” and python_version < “3.12”’ don’t match your environment
Ignoring zstandard: markers ‘python_version >= “3.7” and python_version < “3.12”’ don’t match your environment
Traceback (most recent call last):
File “”, line 1, in
File “/home/aj/Usegalaxy/galaxy/lib/galaxy/util/init.py”, line 54, in
import requests
ModuleNotFoundError: No module named ‘requests’
Galaxy starts fine under python 3.12 afaik, what OS are you using?
ubuntu 24.04 LTS
" lib2to3" package is deprecated from python 3.10. The default version of python in ubuntu 24.04 is python 3.12.4. So it is not working. When I installed python 3.9 and made 3.9 as default, all the apps including Terminal stopped working.
how have your rectified this issue?
The fact is that Galaxy supports Python 3.8 and higher all the way to the latest release. If you are unable to install Galaxy’s python dependencies on your system you either have a VERY weird system or misconfigured python. If you have specific position in the log where you see errors, please post it as a new question and we will check it out.