MALVIRUS-data

SARS-CoV-2 variant catalog accompanying MALVIRUS.

The workflow Snakefile updates the NCBI-based SARS-CoV-2 catalog integrated in MALVIRUS. Only users that have write access to the MALVIRUS-data repo (this one) should run this script.

Requirements

Utility unzip must be available system-wide since the one available in conda does not handle zip files created by NCBI. The one provided by Debian (and derivative) packages works correctly.

Instructions

Clone this repository:

git clone git@github.com:AlgoLab/MALVIRUS-data.git

Create and activate the conda environment shipped with this repository:

conda env create -f environment.yml --prefix ./local-env
conda activate ./local-env

Finally, run Snakemake

make -C software
snakemake -j4 --use-conda -pr

The script will compile the required software, download the data from NCBI, build the updated catalogs.

Then, commit the results.