q2-viromics

A QIIME 2 Plugin for Viromics Identification and Analysis.

Installation instructions

Install Prerequisites

Miniconda provides the conda environment and package manager, and is currently the only supported way to install QIIME 2. Follow the instructions for downloading and installing Miniconda.

After installing Miniconda and opening a new terminal, make sure you're running the latest version of conda:

conda update conda

Install development version of q2-viromics

Clone the repository:

git clone https://github.com/bokulich-lab/q2-viromics.git
cd q2-viromics

Then, run:

mamba create -n q2-viromics2 -c conda-forge -c bioconda -c https://packages.qiime2.org/qiime2/2023.7/core/passed/  -c defaults q2-types numpy=1.23.5 q2cli virsorter=2 "python=3.8" scikit-learn=0.22.1 pandas seaborn hmmer==3.3 prodigal=2.6 screed=1 ruamel.yaml click pip last ncbi-genome-download checkv pyhmmer

After this completes, activate the new environment you created by running:

conda activate q2-viromics

make install

make dev
qiime dev refresh-cache