Execution - epigen/MrBiomics GitHub Wiki

Run the {module} from within the Snakemake conda environment and the module's root directory.

1. Activate the snakemake conda environment, because Snakemake commands only work from within the snakemake conda environment.

   conda activate snakemake
   

2. Enter the {module}/ directory and always execute from within the top level of the module directory.

   cd {module}
   

3. Execute the module, while using conda to install and manage the required software. The flag is not necessary if you are using a global profile and have set the respective environment variable before (see Installation).
   1. Local Execution with one core.

      snakemake --software-deployment-method conda --cores 1
      

   2. Cluster (Non-local) Execution by using a global Snakemake profile containing the execution configuration e.g., number of threads to be used (not necessary if you set it as an environment variable before).

      snakemake --software-deployment-method conda --profile path/to/your/global/profile/
      

[!NOTE] Snakemake global profiles configure default command line arguments (CLI), including resource usage for the relevant executor and storage plugins. They are the interface between an OS-agnostic Snakemake workflow and the infrastructure it is executed on (e.g., SLURM HPC).