Getting Started

Requirements

snakemake>=3.5

python>=3.3

biopython>=1.77

diamond BLAST version>=0.9.32

mafft>=7.429

fasttree>=2.1.10 and/or:

iqtree>=1.6.11

ncbi-genome-download>=0.3.0

Python scripts from this github folder

Installation

Use conda to install snakemake to a Linux or Mac OSX environment:

To install conda:

Install conda here https://conda.io/en/latest/miniconda.html

Install dependencies via conda

Install snakemake:

conda install -c conda-forge mamba

mamba create -c conda-forge -c bioconda -n snakemake snakemake

conda activate snakemake

snakemake –help

Install the ribosomal protein tree workflow from github:

git clone XXX

cd XXX