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.

See also

Additional information on BacterialTyper configuration and requirements

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:

jsanchez@debian:~$ BacterialTyper config

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

Module BacterialTyper config
Parameters:

  • option (string) – State whether to check or install missing modules, packages and third party software. Provide: check/install

  • install_path (string) – Absolute path to install modules or packages missing. Default: BacterialTyper environment path.

  • IslandPath (boolean) – True/False for checking additional perl and software required by this option analysis.

  • debug (boolean) – True/false for debugging messages.

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.

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 [1]) that we distribute along BacterialTyper. See additional details in the API section for Third-party Software and additional requirements in Third-party requirements. As an example:

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