NAME

Package configuration_handler - Handle configuration files of the pipeline


SYNOPSIS

Contains all functions to handle configuration files used in the pipeline.

Provided functions :


EXPORT

Exported functions :


FUNCTIONS

check_provided_file

Check the reference file and the other files or directorie provided by the user. If there are some directories : get the fasta files within it.

get_software_availability

The function will read the configuration file which contains both the command line to execute a software and its options

test_software

The function will test if the path to execute the software is good (existence + execution).

test_configuration_file

The function will execute 2 tests on the configuration file : presence and the fact that the file is readable.


AUTHOR

Benjamin Grenier-Boley <benjamin.grenier-boley@inria.fr>