Command Line Interface ================================== `BV-BRC `_ is an integration of different types of data and software tools that support research on bacterial and viral pathogens. The typical biologist seeking access to the BV-BRC data and tools will usually explore the web-based user interface. However, there are many instances in which programatic or command-line interfaces are more suitable. For users that wish command-line access to BV-BRC, we provide the tools described in this document. We call these tools the *P3-scripts*. They are intended to run on your machine, going over the network to access the services provided by BV-BRC. Installing the CLI Release -------------------------- Since the CLI tools run on your computer, to use them you will need to download and install a software package in order to use them. We currently have Windows, macOS and Debian/Ubuntu releases of the BV-BRC Command Line Interface. The releases are available at the `BV-BRC github site `_. Full installation instructions are available in :ref:`cli-installation`. Tutorials and Reference Documentation ------------------------------------- In order to enable users to make the most of the BV-BRC command line interface we have collected a number of tutorials and reference materials. This collection is linked below. .. toctree:: :maxdepth: 1 :caption: Tutorials: cli_installation cli_getting_started cli_services cli_common_tasks cli_clustering cli_signature_clusters .. toctree:: :maxdepth: 1 :caption: Reference documentation: command_list/index RAST Tutorials -------------- We are also making available here a set of tutorials that relate to the RAST and RASTtk projects. The RAST technology underlies the genome annotation services provided by BV-BRC. .. toctree:: :maxdepth: 1 :caption: RAST tutorials: rasttk_getting_started rasttk_incremental_commands