.. ############################
.. _config-description:

config
======

The ``BacterialTyper`` pipelines provides this module ``config`` to help the user
to configurate the multiple dependencies and requirements.

We encourage ``BacterialTyper`` users to run this module after the installation to
check whether the multiple requirements and dependencies are fulfilled.

.. seealso:: Additional information on ``BacterialTyper`` configuration and requirements

   - :doc:`Installation <../installation/installing>` 
   
   - :doc:`Requirements <../installation/requirements>` 
   
   - :doc:`config module (API) <../../api/modules/config>`


How to run the config module
----------------------------

Once you have installed ``BacterialTyper`` you should be able to run in the command line the pipeline.

If you type ``BacterialTyper`` or ``BacterialTyper.py`` you should see a prompt with the different modules 
available. Following the pipeline name type the module of interest, in this case, config. As an example:

.. code-block:: sh

   jsanchez@debian:~$ BacterialTyper config 

The different options and parameters for this module should appear in the command line prompt. Here we summarized them:


.. function:: Module BacterialTyper config
   
   :param option: State whether to check or install missing modules, packages and third party software. Provide: check/install 
   :param install_path: Absolute path to install modules or packages missing. Default: ``BacterialTyper`` environment path.
   :param IslandPath: True/False for checking additional perl and software required by this option analysis.
   :param debug: True/false for debugging messages.

   :type option: string 
   :type IslandPath: boolean
   :type install_path: string 
   :type debug: boolean 

Basically, this ``BacterialTyper config`` module allows the user to check if the requirements are fulfilled
or try to install them in a given directory (option ``--install_path PATH``) or, as a default, in the python 
environment path. 

.. code-block:: sh

   jsanchez@debian:~$ BacterialTyper config check
   
   jsanchez@debian:~$ BacterialTyper config install
   
   jsanchez@debian:~$ BacterialTyper config install --install_path /some/path/as/example

Additionally, it also includes the check (not the installation) of the different requirements of
a third-party optional analysis of pathogenic islands (option ``--IslandPath``). This analysis is generated by 
IslandPath-Dimob (IslandPath_ :cite:`Bertelli2017`) that we distribute along ``BacterialTyper``. 
See additional details in the API section for :ref:`Third-party Software<third-party-soft>` and 
additional requirements in :ref:`Third-party requirements<third-party-requirement>`. As an example:

.. code-block:: sh

   jsanchez@debian:~$ BacterialTyper config install --IslandPath --debug 






.. include:: ../../links.inc