snakemake and conda environments

Question

Question: how do I specify a conda environment with a distinct prefix in a snakemake rule without it crashing upon trying to deactivate the env?

background: I have conda environments stored in an alternate location (I made a given conda environment with conda create --prefix ./envname) than my baseline miniconda. I call these conda environments in their respective snakemake rules, as advised in the documentation.

rule hello: input: ... output: ... conda: "/path/to/conda/env" shell: "..."

I am unable to supply .yaml files to my Snakefile.

All my snakemake rules run beautifully. However, snakemake then tries to exit and does it using --name not --prefix

subprocess.CalledProcessError: Command 'conda env export --name '/path/to/env'' returned non-zero exit status     1.

Of course this will fail because conda environments referred to by 'name' can't have '/' in them.

So my snakemake crashes. My rules work great in the command line but I'm working with hundreds of samples so I need snakemake.

Also, I know people have said online that you can't do 'conda activate env' and that the workaround is to put a header saying 'source $HOME/miniconda3/etc/profile.d/conda.sh' which I have but this isn't fixing the issue because its within the Snakefile.

help! thank you!