Command Line Interface

PATRIC is an integration of different types of data and software tools that support research on bacterial pathogens. The typical biologist seeking access to the PATRIC 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 PATRIC, 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 PATRIC.

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 PATRIC Command Line Interface.

The releases are available at the PATRIC3 github site. Full installation instructions are available in Installing the PATRIC Command Line Interface.

Tutorials and Reference Documentation

In order to enable users to make the most of the PATRIC command line interface we have collected a number of tutorials and reference materials. This collection is linked below.

Tutorials:

• Installing the PATRIC Command Line Interface
• Using the PATRIC Command-line Interface
• Using PATRIC 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:

• PATRIC 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 PATRIC.

RAST tutorials:

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