Conda and Mamba Installation Problem. Urgent!

Discngine / fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).

MIT License

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Conda and Mamba Installation Problem. Urgent! #123

Closed drorhunvural closed 6 months ago

drorhunvural commented 6 months ago

Bug

There hasn't been any issue with using !conda install fpocket or !mamba install fpocket for a long time. Currently, both of them are giving errors, and the installation process cannot be completed. Fpocket can no longer be used in this way on Google Colab. The problem is caused by the latest update of Google Colab. You can track the Cudatoolkit issue here.

Updating Fpocket to be compatible with the latest version of Google Colab will make it usable again. I believe that you will implement the necessary modifications for this issue.

Screenshots

pschmidtke commented 6 months ago

Why on earth is cuda necessary here? @simonbray do you happen to have an idea by any chance :)

simonbray commented 6 months ago

Why on earth is cuda necessary here? @simonbray do you happen to have an idea by any chance :)

My best guess is that that cudatoolkit and fpocket have a common dependency somewhere but require different versions of it. I don't think this is our job to fix though.

I don't know anything about Google Colab but in general I would create a new conda environment and install fpocket there.

pschmidtke commented 6 months ago

indeed looks like google colab dep issue, not fpocket. I'll try a conda install fpocket on an isolated env to double check

pschmidtke commented 6 months ago

the latest one still needs to be pushed, but fpocket on conda is working if run on a local conda. So as @simonbray suggested, looks like an issue on colab or other, not fpocket related. Will close the issue here

drorhunvural commented 6 months ago

Currently, Conda Forge has not started building the cudatoolkit version 12.2. I believe it will be resolved in the future. You can follow the progress on the related Issue thread here

No action is required from Fpocket for now. This post serves primarily as an informational update for users of Fpocket

simonbray commented 5 months ago

Can you install any other packages using conda or mamba?

edit: this was in reply to @drorhunvural's previous comment before he edited.