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AlexanderLabWHOI / eukrhythmic

A metatranscriptomic pipeline optimized for the study of microeukaryotes.
MIT License
15 stars 3 forks source link

Conda environments for individual modules / rules #4

Closed halexand closed 4 years ago

halexand commented 4 years ago

I think that we should split up environment.yaml into individual, specified environment files. (e.g. Trinity rules will have their own trinity.yaml file in envs/). I think that this lessens the likelihood of issues with building the conda environment and running into conflicts between programs (e.g. Busco).

This is a good to-do for next weeks code review @akrinos @cnatalie

halexand commented 4 years ago

I am thinking that the main environment.yaml should just have pandas, snakemake, and the like.

akrinos commented 4 years ago

added yaml files for each rule in envs/ and eliminated unnecessary packages in environment.yaml (old entries commented out for now).

akrinos commented 4 years ago

Note that for some reason with creating this many environments, snakemake appears to sometimes exit the first time you run the pipeline...