Execution - epigen/MrBiomics GitHub Wiki
Run the {module}
from within the Snakemake conda environment and the module's root directory.
- Activate the snakemake conda environment, because Snakemake commands only work from within the snakemake conda environment.
conda activate snakemake
- Enter the
{module}/
directory and always execute from within the top level of the module directory.cd {module}
- 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).
- Local Execution with one core.
snakemake --software-deployment-method conda --cores 1
- 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/
- Local Execution with one core.
[!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).