This profile configures snakemake to run discover virome workflow in slurm (tested) cluster system. Discover-profile profile is based on generic Snakemake-Profile and in princible can be used also on lsf and pbs cluster system. The mapping between snakemake ressources and cluster submission can be configured in the cluster_spec.yaml. Default values are used for all rules not having the snakemake ressource paremeters.
The units are minutes and GB but can be changed.
To deploy this profile,
mkdir -p ~/.config/snakemake
cd ~/.config/snakemake
git clone git@github.com:avilab/discover-profile.git
Then, you can run Snakemake with
snakemake --profile discover-profile ...
so that jobs are submitted to the cluster. If a job fails, you will find the "external jobid" in the Snakemake error message. You can investigate the job via this ID. Checking slurm status (slurm_status.py) is currently commented off in config.yaml.