06. Run LongSom

After installing (do not forget to activate the conda environment) and preparing the input, you are now ready to use LongSom.

LongSom is using Snakemake and was designed to run multiple samples in parallel on an HPC. If you are new to snakemake, we recommend visiting Snakemake's documentation

First time

If running LongSom for the first time, you first need to install rule-specific environments.

For this, from the LongSom directory run:

snakemake -s snakemake -s workflow/Snakefile --use-conda --conda-create-envs-only --configfile config/config.yaml

Then, make the bash script to run the workflow run_LongSom.sh executable:

chmod +x run_LongSom.sh

or, if you are using a Slurm Workload Manager:

chmod +x run_LongSom_slurm.sh

Usage (Slurm)

LongSom was originally designed for the Slurm Workload Manager and this is the preferred way to use it. If your HPC does not use Slurm, see below. If your cluster is using a Slurm Workload Manager, LongSom can simply be run as:

./run_LongSom_slurm.sh

Usage (Not Slurm)

LongSom can be run locally with the following command, this is however not recommended:

./run_LongSom.sh

If you are using a job scheduler other than Slurm, please visit Snakemake's plugin catalog, pick the one corresponding to your system (e.g. LSF), install it and modify the snakemake command in run_LongSom.sh accordingly. LongSom's maintainers will likely not be able to help as they do not have access to any other system than Slurm.