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.
The PATRIC CLI distribution is available at the PATRIC github releases page. New releases typically come out for MacOS first. We currently also support Debian/Ubuntu Linux and plan support for CentOS Linux and Windows.
The PATRIC CLI tutorial is available here.
Please note: If you run into permission problems starting the PATRIC app on your Mac, you can still use the CLI. The PATRIC app is a little wrapper around bringing up a Terminal window configured properly, and we can this by hand.
To do this, start Terminal.app and use Cmd-N if necessary to bring up a new window. Then run the following command in the Terminal window to set up the window for using the PATRIC CLI:
source /Applications/PATRIC.app/user-env.sh