Ward D
Ward D
Hi, Have a look at: https://snakepipes.readthedocs.io/en/stable/content/setting_up.html#configuring-snakepipes TLDR: the conda directory needs to be set on the profile level, which is not (yet ? cfr. #1049 ) changeable through snakePipes config....
Cluster configurations (cluster.yaml) are deprecated by snakemake since quite some time, hence why this is dropped from snakePipes now as well. There is some overlap with profiles, though. If your...
As of 3.0.0 condaEnvDir should not be set in defaults.yaml anymore, but should be set in the appropriate profile (wherever that lives). defaults.yaml points to the local profile by default,...
> from my point of view, the user should be able to edit the config shipped with snakePipes. This is what the `snakePipes config` function is for. I'd just update...
Makes sense yea, thanks ! 👍🏼
Obsolete since cluster yamls have been deprecated.
These were most likely due to trailing slashes in the conda path. Should be fixed in #1041
Is this something reproducible ? I.e. does re-running createEnvs keep resulting in the same behavior ?
If you try the --only flag to install other environments aside from the rna-seq one, do these get installed properly ?