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Setup

We start by setting up our machine with required tools and packages to get it ready for executing the workflow. We primarily need the following tools

  • Miniconda
  • Qiime2 (2025.4.0)
  • Snakemake
  • Snakemake wrapper utils
  • Pytest

To speed up the installation, we will use an environment.yml file exported from a conda environment that successfully executed the workflow. .

You can create a new environment using the following command. This will create a environment with name qiime2_amplicon_snakemake.

conda env create -f ../envs/environment.yml

Note

To execute this command you need to have either Miniconda or Anaconda installed on your system.