Add complete conda env to faster solving

[maxulysse]

nf-core/sarek pull request

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[maxulysse]

@apeltzer any idea on how to simplify the environment.yml file?

[apeltzer]

I've recently read something about removing detailed dependencies wherever possible as this makes the solving faster. E.g. if you have samtools which depends on htslib, then don't explicitly import htslib and let the samtools recipe take care of finding htslib and installing it for you.

I'd try to only have the "major" packages in the environment.yaml and then try to find out whether this builds in the end then ...?

[apeltzer]

Its quite a long list now - really focus on the major ones and hope that it resolves it properly. Also I heard mixed experiences with having R packages that are not from conda-forge + bioconda but also from other R channels to be largely incompatible with these :-(

[maxulysse]

I actually have no idea, I just copied the environment that was successful in mamba here.
I was happy that it worked already

[maxulysse]

Ok, so I'll try to remove as much as possible and see if it still works as well.
Thanks for the tips

[apeltzer]

Yes, I think that would make sense 👍🏼 Otherwise updating this will be extremely difficult :-(

[maxulysse]

Yes, I think that would make sense 👍🏼 Otherwise updating this will be extremely difficult :-(

I don't plan on updating this ever actually.
Plan is to get rid of it once 2.7 is done and go full dsl2 for 3.0

[apeltzer]

Much better :-)

[maxulysse]

Definitively better, but in the end, I have no idea why it's working when the previous version was not.

[apeltzer]

Mistery conda ;-)