NBIS Metagenomics Workflow¶
This is a snakemake workflow for preprocessing and analysis of metagenomic datasets. It can handle single- and paired-end data and can run on a local laptop with either Linux or OSX, or in a cluster environment.
1. Clone the repository Checkout the latest version of this repository (to your current directory):
git clone firstname.lastname@example.org:NBISweden/nbis-meta.git cd nbis-meta
To create the environment
nbis-meta use the supplied
mkdir envs/nbis-meta conda env create -f environment.yaml -p envs/nbis-meta
Next, add this directory to the envs_dirs in your conda config (this is to simplify activation of the environment and so that the full path of the environment installation isn’t shown in your bash prompt):
conda config --add envs_dirs $(pwd)/envs/
Activate the environment using:
conda activate envs/nbis-meta
You are now ready to start using the workflow!
If you plan on using the workflow in a cluster environment running the SLURM workload manager (such as Uppmax) you should configure the workflow with the SLURM snakemake profile. See the documentation.