Do not use a shared conda environment for running snakemake

UCSF-DSCOLAB / data_processing_pipelines

A repository to store the existing pipelines to process the various CoLabs datasets

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Closed amadeovezz closed 3 months ago

amadeovezz commented 4 months ago

The current approach to running snakemake on c4 leads to undesirable behavior.

We need to:

Create a conda file with all the snakemake dependencies + mamba
Modify run_snakemake.sh to load the CBI environment
Modify run_snakemake.sh to create an insolated snakemake environment using the conda file