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JLSteenwyk / orthosnap

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
https://jlsteenwyk.com/orthosnap/
MIT License
23 stars 1 forks source link

Snakemake environment build-up for orthosnap. #7

Closed Andyargueasae closed 11 months ago

Andyargueasae commented 11 months ago

Hi,

I am trying to use orthosnap as one part of the snakemake workflow to work out the phylogeny. My colleague built up the conda environment for orthosnap like this:

image

But seems that for some packages especially biopython and tqdm, there is conflict between them. So I wonder for orthosnap, which dependencies are essential that I could keep them?

Sorry for bothering

JLSteenwyk commented 11 months ago

Hi @Andyargueasae,

Thank you so much for choosing OrthoSNAP for your Snakemake workflow.

See here for a YAML file that addresses your need. https://github.com/rbturnbull/orthoflow/blob/master/orthoflow/workflow/envs/orthosnap.yaml

thanks again!