Execution

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

1. activate the snakemake conda environment (Snakemake commands only work from within the snakemake conda environment)

   conda activate snakemake

2. enter the {module} directory (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
   1. local execution with one core

      snakemake --use-conda --cores 1

   2. vanilla cluster execution with 32 jobs for cluster engines that support shell scripts and have access to a common filesystem, (e.g. the Sun Grid Engine), see Snakemake Cluster Execution documentation

      snakemake --use-conda --cluster qsub --jobs 32
      

   3. configured cluster execution by using --profile (not necessary if you set it as an environment variable before)

      snakemake --use-conda --profile path/to/cluster_profile
      

Note

Snakemake cluster profiles are the interface between an OS-agnostic Snakemake workflow and the system it is executed on (e.g., SLURM HPC). If you are working on another cluster engine get your cluster execution profile here: The Snakemake-Profiles project