Install and Setup

Tourmaline 2 uses QIIME 2 2024.10 for analysis and Snakemake for workflow management.

Requirements

  • Conda (Miniconda recommended)
  • QIIME 2 (2024.10) amplicon workflow: environment name qiime2-amplicon-2024.10
  • Snakemake conda environment (name example: snakemake-tour2)

Create environments

conda create -c conda-forge -c bioconda -n snakemake-tour2 snakemake biopython yq parallel

Install QIIME 2 (see QIIME 2 docs for OS specifics), ensuring the environment is named exactly:

conda create -n qiime2-amplicon-2024.10  # or use official installer for 2024.10

Optional (BLCA method only):

conda create -c conda-forge -c bioconda -n bt2-blca biopython muscle=3.8 bowtie2

Get Tourmaline 2

git clone https://github.com/aomlomics/tourmaline.git
cd tourmaline

Running requirements

  • Activate snakemake-tour2 when running the pipeline
  • Keep qiime2-amplicon-2024.10 installed (used by Snakemake rules via --use-conda)

Legacy v1

For the legacy pipeline and docs, see the V1 branch and legacy docs referenced in Citation & Legacy.