3 Snakemake workflow management system

3.1 Install snakemake

• Snakemake^[1] software is best installed via the Mamba package manager or Mambaforge.
• We first need to confirm if conda or mamba are installed and proceed from there.

mamba install -c bioconda snakemake

3.2 Install snakemake minimal

mamba install -c bioconda snakemake-minimal

3.3 Install snakemake wrappers

mamba install -c bioconda snakemake-wrapper-utils

3.4 Install SnakeDeploy

• Snakedeploy^[2] deploys a snakemake pipeline from version control like GitHub.

mamba install -c bioconda snakedeploy

3.5 Installing using environment.yml

name: snakemake
channels:
    - bioconda
dependencies:
    - snakemake =7.19.1
    - snakemake-minimal =7.19.1
    - snakedeploy =0.8.6
    - snakemake-wrapper-utils =0.5.0

conda activate base
mamba env create --name snakemake --file environment.yaml