[24.1] Remove defaults channel for conda usage #18859
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https://www.theregister.com/2024/08/08/anaconda_puts_the_squeeze_on/ According to the FAQs on https://repo.anaconda.com/pkgs/ this includes `pkgs/main`, `pkgs/r`, and `pkgs/msys2`. Seems also to be a good idea because for `mulled_channels` we apparently never used it (consistency).
to use miniforge
can be installed manually by affected users
Co-authored-by: Nicola Soranzo <[email protected]>
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Not sure if this can be considered a bugfix and therefore qualify for backporting, it's a bit of a gray area. |
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This seems like a troubling thing to backport to me, I would be pretty upset if I was an admin and this just changed in a stable bug fix. Maybe I don't understand though 😢. If you want to encourage people running older Galaxies to do this - isn't encouraging them to set the config values that way a more appropriate, intentional change? |
Agreed, we could write a short message to post to the relevant admin Matrix channels and mailing lists. |
Yeah .. I primarily thought about planemo. If I remember right planemo uses the For admins a note to
Sorry. Here is the story (as far as I got it): The company behind conda (silently) changed their terms of service in 2020. Basically the My conclusion for planemo is that it's not safe to use as long as we use miniconda and the defaults channel. For point 3 of my list above I'm not entirely sure if this is needed. Maybe not for environments older than 2020. Our HPC admins, e.g., will remove all conda envs that made use of the defaults channel (probably to be on the safe side). And I'm really wondering about the containers at biocontainers... |
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If this about Planemo - I feel like the appropriate change is to override the default when launching Galaxy from Planemo. It already has the ability to set these options right? Maybe instead of leaving them null or whatever we do to defer to Galaxy we set them to explicit values for a few releases? |
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I would also propose putting it into dev. If its important for planemo we can for the time being point to a backported branch (this branch here), let planemo depend on a pre-release, or just change the defaults as John mentioned. With the |
To clarify, it's already in dev, this is a backport. |
It's already in
If we use this branch, installations like usegalaxy would use the change. I think is that is what @jmchilton wants to avoid (for good reasons). Creating another brach from 24.1 seems to be the best solultion for me. But we would need a new (pre)release of the packages and a new release of planemo.
Problem is that we still install miniconda which constructs its base environment using the This worries me for instance for the CI in our company maintained tool repo and for my usage in See also recent discussion on matrix. |
are they possibly using |
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If you strip out the change to |
Yep. Some of them do.
That might be a good compromise. Then |
To get rid of the potential problem with the default channel in planemo usage and up-to-date installations I would suggest a backport. Instead of 24.1 we could also got further back.
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