Skip to content

Installation Guide

install with bioconda

VirMet is available through Bioconda, a channel for the conda package manager. Once conda is installed and the channels are set up, you can install the package with all its dependencies by doing:

conda install virmet

Dependencies

If you don't want to install VirMet the easy way with conda install virmet (which is highly recommended), try the classic:

pip install virmet

This should also work. However, VirMet relies on several third-party tools used to access databases, trim, convert, filter and map reads. These will need to be installed manually.

Python and python dependencies:

  • python >=3.9
  • biopython (already installed with the pip command)
  • numpy (already installed with the pip command)
  • pandas (already installed with the pip command)
  • requests (already installed with the pip command)

Third-party tools:

  • blast >=2.3
  • bwa
  • fastp
  • htslib
  • kraken2 >=2.1.6
  • ncbi-datasets-cli
  • r-ggplot2
  • samtools >=1.3
  • seqkit
  • seqtk

Please, note that these tools are all automatically available if VirMet is installed with conda install virmet.