Hi,
I have installed nef-pipelines in a Macbook with M2 following the instructions on the NEF=Pipelines website GitHub - varioustoxins/NEF-Pipelines: Nef tools.
The installation went smooth and gave the message:
installed package nef-pipelines 0.1.95, installed using Python 3.9.6
These apps are now globally available
- nef
done! 
but when running nef, I get the following error:
/Applications/ccpnmr3.2.5/miniconda/bin/python3: can’t open file ‘/Applications/ccpnmr3.2.5/miniconda/lib/python3.10/site-packages/nef_pipelines/main.py’: [Errno 2] No such file or directory
any help?
Thanks in advance.
Francisco
1 Like
Hi Franscisco
Could you let me know what operating system and version you are running
Mac and version or
Linux distribution and version
Also could you paste in the message you see at the top of your console when you open it [use double space bar as a shortcut]
You should see something like
Jupyter QtConsole 5.3.2
Python 3.10.9 | packaged by conda-forge | (main, Feb 2 2023, 20:24:27) [Clang 14.0.6 ]
Type ‘copyright’, ‘credits’ or ‘license’ for more information
IPython 8.12.2 – An enhanced Interactive Python. Type ‘?’ for help.
As it appears that you have python 3.9.6 but the nef script is looking for a distribution which is 3.10, this maybe a bug in our script
Regards
Gary
Dr Gary S Thompson NMR Facility Manager
CCPN CoI & Working Group Member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Division of Natural Sciences
University of Kent, Canterbury, Kent, England, CT2 7NZ
:01227 82 7117
: g.s.thompson@kent.ac.uk
orchid: ORCID
Dear Gary,
I am running a Mac M2 with OS 14.4.1 (Sonoma).
Nef does not start at all. After installation, I type %nef in the terminal to test the installation but It just give the message pasted above.
Python 3.10 seems to be present under my ccpnmr directory: /Applications/ccpnmr3.2.5/miniconda/lib/python3.10/site-packages
but nef_pipelines/main.py does not exists.
Regards,
Francisco
If I start python, the message is:
Python 3.10.9 | packaged by conda-forge | (main, Feb 2 2023, 20:26:08) [Clang 14.0.6 ] on darwin
Type “help”, “copyright”, “credits” or “license” for more information.
Regards,
Francisco
Hi Francisco
- looking at this some more are you typing %nef of nef in the command line? It should be nef without a % in front, the % is just part of your command prompt
- When you get the error
/Applications/ccpnmr3.2.5/miniconda/bin/python3: can’t open file ‘/Applications/ccpnmr3.2.5/miniconda/lib/python3.10/site-packages/nef_pipelines/main.py’: [Errno 2] No such file or directory
This is because you installed nef pipelines outside of ccpnmr but ccpnmr’s own internal script is trying to run nef for you using miniconda but its not installed, I have given ed a modified nef script that avoids this problem but I don’t think they have been incorporated yet
Try the following
mv /Applications/ccpnmr3.2.5/bin/nef /Applications/ccpnmr3.2.5/bin/ccpn_nef
After this hopefully it should all work, however I have found a couple of bugs in the last few days so I would try a quick
pipx upgrade nef-pipelines
To pull down the latest updates and and then give it another go with
nef test
To see fit it is all working on your machine
I hope that helps
regards
Gary
Dr Gary S Thompson NMR Facility Manager
CCPN CoI & Working Group Member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Division of Natural Sciences
University of Kent, Canterbury, Kent, England, CT2 7NZ
:01227 82 7117
: g.s.thompson@kent.ac.uk
orchid: ORCID
Excellent! Let me know if you have any questions or need any help, please note the tutorial on the CCPN website is somewhat out of data and I am working on new material / an update (later this week?)
regards
Gary
Dr Gary S Thompson NMR Facility Manager
CCPN CoI & Working Group Member
Wellcome Trust Biomolecular NMR Facility
School of Biosciences, Division of Natural Sciences
University of Kent, Canterbury, Kent, England, CT2 7NZ
:01227 82 7117
: g.s.thompson@kent.ac.uk
orchid: ORCID