Using SPRAS

SPRAS is run through Snakemake, which comes with the SPRAS conda environment.

To run SPRAS, run the following command inside the spras directory, specifying a config.yaml and the number of cores to run SPRAS with:

snakemake --cores 1 --configfile config.yaml

Parallelizing SPRAS

SPRAS works on any specified number of cores, and will, thanks to Snakemake, automatically know how to best distribute work across various cores to finish work specified in a configuration as fast as possible.

To parallelize SPRAS, specify --cores to be a value higher than 1:

snakemake --cores 4 --configfile config.yaml

SPRAS also supports high-performance computing with its integration with HTCondor. See Running with HTCondor for more information.