Usage

Basic usage of ursa follows four steps. Ursa has substantial computational and storage requirements. Refer to the resources information before undertaking a project.

Initialize

First, initialize a project. This will create a directory in which all project files are located.

ursa initialize <name>

Ursa will create a directory called <name> within the directory from which the command is issued. Ursa will also complete initialization steps such as downloading required Clawpack and D-Claw source code and copying the snakefile and config file into the expected location within the project directory.

Modify

Before running ursa, the user must modify the configuration file to provide required input information. See configuration for details. In addition, make sure that you have navigated to the directory which was created in the initialize step.

Run

After configuration, run ursa. This may be done by executing the following command:

ursa run all

This is equivalent to running:

snakemake -s workflow/Snakefile --use-conda --benchmark-extended --cores 4

Snakemake has many command line arguments that may be passed at runtime. Refer to its documentation for details.

Evaluate

Upon completion, evaluate the quality control files and review results.