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hoelzer-lab / ribap

A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
GNU General Public License v3.0
19 stars 3 forks source link

conda environment of roary is not resolving #39

Closed klamkiew closed 1 year ago

klamkiew commented 1 year ago

see title, I am working on it ;)

hoelzer commented 1 year ago

Argh, what's going on with all theses condo envs ^^ damn it

klamkiew commented 1 year ago

Sigh https://github.com/sanger-pathogens/Roary/issues/585 It's not me/us - seems to be a general issue.

klamkiew commented 1 year ago

Funnily enough, I can resolve the env with mamba... not sure why conda is having issues here.... maybe we can plug in mamba into NF, even though it is experimentally? @hoelzer ever done this before? :D

hoelzer commented 1 year ago

Yes Mamba profiles work, Marie implemented one in... Clean I think? Or rnaflow? We can ask her and c&p ;)

hoelzer commented 1 year ago

And strange the roary condo thing... Good we build also a container 3y ago ^^

klamkiew commented 1 year ago

Once I find some time, I'll try to dig deeper into that issue; for now, maybe the mamba fix is already sufficient. But we also had issues with the prokka env, so I think there might be some underlying conda config problem :/

klamkiew commented 1 year ago

Alright; I set useMamba = true in the conda scope of our nextflow config. Now, one has to have nextflow and mamba, if one wants to use conda, but this isn't much of a hussle with conda anyways. Closing this for now -- I still have to check whether a switch between conda and mamba is possible (e.g. a profile mamba, that looks like conda but uses mamba)

hoelzer commented 1 year ago

great thx!

Honestly, for me it's also totally fine if the user needs nextflow +

and conda is not natively supported. Of course, if we can have a profile that looks like conda but just installs and uses mamba: fine ;) But maybe not worth the hazzle

klamkiew commented 1 year ago

Use Mamba to resolve packages It is also possible to use mamba to speed up the creation of conda environments. For more information on how to enable this feature please refer to Conda.

Warning This feature is experimental and may change in a future release.

https://www.nextflow.io/docs/edge/conda.html#use-mamba-to-resolve-packages Fingers are crossed, nothing too dramatically changes ;) I agree with you, but we should keep it in mind.