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1. Prerequisites

Authors
Affiliations
Department of Biology, San Diego State University, San Diego, California, USA
Department of Biology, San Diego State University, San Diego, California, USA

1.1 Conda/Mamba

Ensure you have conda/mamba installed on the system you intend to run the workflow on. A detailed mamba installation guide can be found here. For cluster environments, please contact your system administrator for conda/mamba usage and environment setup.

Verify your conda/mamba installation with:

# Verify conda works with
conda --version

# Verify mamba works with
mamba --version

1.1.1 Snakemake Conda/Mamba environment

Once your conda/mamba environment is working, you should create a new conda/mamba environment and install snakemake with the following command.

mamba create -n snakemake -c bioconda snakemake>=9.11.0

Once the environment is created, test your snakemake installation.

mamba activate snakemake
snakemake --version
# This should report a snakemake version greater than 9.11.0
SaVor
SaVor
SaVor
2. Workflow Download and Setup