Installation

Prerequisites

ViralQC requires Python 3.8 or higher (but lower than 3.12) and several bioinformatics dependencies.

Installation via pip

Step 1: Install Dependencies

First, install the required dependencies using micromamba or conda:

micromamba install \
  -c conda-forge \
  -c bioconda \
  "python>=3.8.0,<3.12.0" \
  "snakemake-minimal>=7.32.0,<7.33.0" \
  "blast>=2.16.0,<2.17.0" \
  "nextclade>=3.15.0,<3.16.0" \
  "seqtk>=1.5.0,<1.6.0" \
  "ncbi-datasets-cli>=18.9.0,<18.10.0" \
  "taxonkit>=0.20.0,<0.21.0"

Dependency Descriptions:

Package	Version	Description
Python	≥3.8.0, <3.12.0	Base programming language
Snakemake	≥7.32.0, <7.33.0	Workflow manager for analysis orchestration
BLAST	≥2.16.0, <2.17.0	Sequence similarity search tool
Nextclade	≥3.15.0, <3.16.0	Clade analysis and quality control tool
Seqtk	≥1.5.0, <1.6.0	Utility for processing FASTA files
NCBI Datasets CLI	≥18.9.0, <18.10.0	Tool for downloading data from NCBI
TaxonKit	≥0.20.0, <0.21.0	Utility for NCBI taxonomy manipulation

Step 2: Install ViralQC

pip install viralQC

Step 3: Verify Installation

vqc --help

You should see the ViralQC help message listing the available commands.

Installation from Source Code

Step 1: Clone the Repository

git clone https://github.com/InstitutoTodosPelaSaude/viralQC.git
cd viralQC

Step 2: Create Conda Environment

micromamba env create -f env.yml
micromamba activate viralQC

Step 3: Install ViralQC

pip install -e .

Step 4: Verify Installation

vqc --help

Docker

We provide a Dockerfile to build a container with all the dependencies installed as well as with the viralQC datasets.

Step 1: Clone the Repository

git clone https://github.com/InstitutoTodosPelaSaude/viralQC.git
cd viralQC

Step 2: Build the Docker Image

docker build -t vqc .

Step 3: Verify Installation

docker run vqc --help

Step 4: Run viralQC

You can run viralQC using the following command:

 docker run \
  -v $(pwd)/test_data:/app/test_data \
  -v $(pwd)/test_outputs:/app/outputs \
  vqc run \
  --input /app/test_data/sequences.fasta -v

Where the volumes of input and output directories are mounted to the container.