Command Line Interface
==================================

`PATRIC <https://www.patricbrc.org>`_ 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 <https://github.com/PATRIC3/PATRIC-distribution/releases>`_. Full installation
instructions are available in :ref:`cli-installation`.

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.

.. 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 PATRIC.

.. toctree::
    :maxdepth: 1
    :caption: RAST tutorials:

    rasttk_getting_started
    rasttk_incremental_commands