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 Installing the BV-BRC Command Line Interface.

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.

Tutorials:

• Installing the BV-BRC Command Line Interface
• Using the BV-BRC Command-line Interface
• Using BV-BRC Services from the Command Line
• Common Tasks With P3 Scripts
• Looking for Hypothetical Proteins in Clusters of Related Features
• Computing Signature Clusters: an Application of the Command-Line Tools

Reference documentation:

• BV-BRC Command Line Program Reference

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.

RAST tutorials:

• RASTtk: Getting Started With The Default Pipeline
• RASTtk, The Incremental Commands