Using SPRAS

SPRAS is run through Snakemake, which comes with both the SPRAS conda environment and as a dependency of SPRAS.

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

spras run --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:

spras run --cores 4 --configfile config.yaml

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