Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Sketchlib back end not available? #278

Open
hayleyjaywilson opened this issue Jul 21, 2023 · 8 comments
Open

Sketchlib back end not available? #278

hayleyjaywilson opened this issue Jul 21, 2023 · 8 comments
Labels
package Packaging of code

Comments

@hayleyjaywilson
Copy link

Versions
Poppunk V2.6.0
poppunk_sketch --version respectively.
Alternatively, please post the output of conda list in your environment -->

Command used and output returned
poppunk --create-db --r-files reference_list.txt --output strain_db --threads 8 --plot-fit 5

error:
mash: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory
Sketchlib backend not availableNeed mash v2 or higher

Describe the bug
I am not sure what has happened. I followed the install instructions for the pp_env - so a fresh environment.
I have tried updating python, pp_sketchlib and poppunk but no joy. But the software will not run even if I attempt to manually install.

Also poppunk_sketch --version returns:
-bash: poppunk_sketch: command not found

I am not sure what the issue with the install is (apologies if it is obvious)

Many thanks
@johnlees
Copy link
Member

How did you install PopPUNK, can you copy the commands you ran?

@hayleyjaywilson
Copy link
Author

hayleyjaywilson commented Jul 21, 2023 via email •
edited
Loading

@johnlees
Copy link
Member

Can you also give the output of conda list?

@hayleyjaywilson
Copy link
Author

hayleyjaywilson commented Jul 21, 2023 via email •
edited
Loading

@johnlees
Copy link
Member

And can you also try running:

sketchlib --version

@hayleyjaywilson
Copy link
Author

hayleyjaywilson commented Jul 30, 2023 via email •
edited
Loading

@johnlees
Copy link
Member

Sorry for my delay too, just back from holiday

What is the result of running ls $CONDA_PREFIX/lib/python3.8/site-packages? Do you see files related to pp_sketchlib?

This is an odd one, I am guessing that the sketchlib library hasn't been installed where it's expected to be. I would suggest trying a new environment using python3.10 as a next step, but this may need a conda clearout. Another alternative could be to try the docker container on quay.io

@hayleyjaywilson
Copy link
Author

hayleyjaywilson commented Aug 16, 2023 via email

@johnlees johnlees added the package Packaging of code label Nov 30, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
package Packaging of code
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@johnlees @hayleyjaywilson