Source code for analysis of hospital wastewater metagenomic data
Welcome to ATTACK-AMR - a bioinformatics pipeline for analysis of hospital wastewater antimicrobial resistance metagenomic data.
This pipeline requires the package manager Conda and the workflow management system Snakemake. All other dependencies are handled automatically by Snakemake.
Download Miniconda3 installer for Linux from here. Installation instructions are here. Once installation is complete, you can test your Miniconda installation by running:
$ conda list
Snakemake recommends installation via Conda:
$ conda install -c conda-forge mamba
$ mamba create -c conda-forge -c bioconda -n snakemake snakemake
This creates an isolated enviroment containing the latest Snakemake. To activate it:
$ mamba init
$ mamba activate snakemake
To test snakemake installation
$ snakemake --help