The BV-BRC is an integration of different types of data and software tools that support research on bacterial 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 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 BV-BRC.
The BV-BRC CLI distribution is available at the BV-BRC github releases page. New releases typically come out for MacOS first. We currently also support Windows and Debian/Ubuntu and CentOS Linux.
The BV-BRC CLI tutorial is available here.
If you need a basic command line tutorial, you can find one here.
Please note: If you run into permission problems starting the BV-BRC app on your Mac, you can still use the CLI. The BV-BRC 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 BV-BRC CLI:
source /Applications/BV-BRC.app/user-env.sh