Issue with tutorial snakemake

[vbx1404]

Description of the bug

foldseek 6.29e2557 does not exist (perhaps a typo or a missing channel)

Command used and terminal output

snakemake --snakefile Snakefile --configfile demo/config_actin.yml --use-conda --cores 8

Relevant files

System information

64-bit windows

[braebigge]

Thanks for bringing this to our attention. We've tried to re-create this issue but have been unable to on our macOS systems. We'll keep digging, but if you have any more info that could help us (did other packages install normally? are you able to install foldseek manually with conda? etc.), that would be much appreciated!

[GBOTR]

@braebigge do you happen to be running on an Intel Mac? I tried to follow the Quickstart guide as well on an M1 Mac and got the same error shown in that first post.

Just to test it, I started an x86 container (under Rosetta emulation) on my Mac and it at least got farther than that install step, so it looks like the CPU architecture has something to do with this error.

[braebigge]

Thanks for looking into this @GBOTR! I personally have an M2 Mac but have an Intel installation of miniconda (using Rosetta as well). So it does seem like it might be related to this, and we'll look into this more!

[alexjisa]

Hi! I have the same problem in my M1 Mac and I am still trying to solve it.

Thank you in advance :)

[mezarque]

It looks like the versions of Foldseek in bioconda might have changed since we originally released the package.

For some reason, rather than 6.29e2557 alone, there are now several versions with that prefix: 6.29e2557-0, 6.29e2557-1, and 6.29e2557-2. I think this might explain why installation of the demo is failing, because we have pinned the 6.29e2557 version.

It's possible that we have locally cached versions of the 6.29e2557 prefix, which allows us to proceed with installation even if the 6.29e2557 no longer exists.

I'm going to work on resolving this and see if altering the version number to match one of the versions available via bioconda will solve the problem.

[mezarque]

This doesn't seem to have been the issue; adding -2 to the end of a version resulted in the same error.

[mezarque]

After doing some further digging, I think the actual issue here might be a different version of conda than we support.

@GBOTR @alexjisa are you using the x86_64 or arm64 version of conda for your Macs? If you install miniconda3, for example, you want to use the version named "Intel x86 64-bit", not "Apple M1 64-bit".

If you install the x86_64 version, that might solve your issue. I don't believe there's an arm64-compatible distribution of Foldseek.

You can check which version you have installed by using conda info, which should print out a long set of parameters. Look for the platform field, which will say:

platform : osx-64

or

platform: osx-arm64