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MikkelSchubert / paleomix

Pipelines and tools for the processing of ancient and modern HTS data.
https://paleomix.readthedocs.io/en/stable/
MIT License
43 stars 19 forks source link

conda environment perpetually solving during installation #50

Closed renhamm closed 1 year ago

renhamm commented 1 year ago

When using the instructions for installing paleomix in a conda environment, the "solving environment" step takes many hours and never finishes, despite many work arounds. Is there something that I am missing? I would prefer to set up everthing an a conda enviroment since I am doing remote htc work.

MikkelSchubert commented 1 year ago

It's definitely not supposed to take that long. I'll look into it before the end of the week and get back to you.

Best, Mikkel

renhamm commented 1 year ago

Thanks! I was able to get it to run once I specified versions for all the channels/dependencies, but that resulted in ~100 conflicts across packages. Currently trying different combinations to see if I can resolve this issue

MikkelSchubert commented 1 year ago

Have you tried using mamba instead of vanilla conda? If not, then I'd highly recommend it. Mamba only takes a few seconds resolve the environment on my system.

I think the problem is that I've consistently been using mamba for a long time, so I didn't notice how bad it had gotten with regular conda. I'll try to see if I cannot improve the situation without having to specify exact versions for everything, but that might end up being the solution.

MikkelSchubert commented 1 year ago

I've attached an alternative conda environment to this message, which should solve the problem by pinning the major and minor versions, but not the point release (${major}.${minor}.${point}). It still takes about 4-5 minutes to resolve with conda on my machine, compared to about 2-3 seconds with mamba, which is not optimal, but it's usable. I could reduce it further by pinning the point releases, but that would result in people missing out on bug-fixes in dependencies in between the (very irregular) paleomix releases.

If mamba isn't an option, or if you have time to test it anyway, then please let me know if it works for you.

paleomix_1_3_8.yaml.txt

renhamm commented 1 year ago

I was able to get things up and running with mamba!

renhamm commented 1 year ago

I got it to work! Thanks!

On Sun, Jul 2, 2023 at 1:44 PM Mikkel Schubert @.***> wrote:

I've attached an alternative conda environment to this message, which should solve the problem by pinning the major and minor versions, but not the point release (${major}.${minor}.${point}). It still takes about 4-5 minutes to resolve with conda on my machine, compared to about 2-3 seconds with mamba, which is not optimal, but it's usable. I could reduce it further by pinning the point releases, but that would result in people missing out on bug-fixes in dependencies in between the (very irregular) paleomix releases.

If mamba isn't an option, or if you have time to test it anyway, then please let me know if it works for you.

paleomix_1_3_8.yaml.txt https://github.com/MikkelSchubert/paleomix/files/11931357/paleomix_1_3_8.yaml.txt

— Reply to this email directly, view it on GitHub https://github.com/MikkelSchubert/paleomix/issues/50#issuecomment-1616812628, or unsubscribe https://github.com/notifications/unsubscribe-auth/AO2GFKXPH7QNR4GKCZ4SBPLXOHMRLANCNFSM6AAAAAAZXSACMA . You are receiving this because you authored the thread.Message ID: @.***>