Package configuration_handler - Handle configuration files of the pipeline
Contains all functions to handle configuration files used in the pipeline.
Provided functions :
check_provided_files
read_configuration_file
test_software
test_configuration_file
Exported functions :
check_provided_files
read_configuration_file
test_configuration_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.
parameters :
$ref, the location of the reference file
$ref_other, the reference on the array containing other files or directories
$content_warning, the content of the warning file
returns : a reference on an hash table containing other files
The function will read the configuration file which contains both the command line to execute a software and its options
parameters :
$configuration_file, the configuration file
$content_warning, the content of the warning file
returns : the command line to execute according to exe path and options read or the empty string if an error occured during the file parsing and the software availability
The function will test if the path to execute the software is good (existence + execution).
parameters : $exe_path, the path to test
returns : the rigth executable path (in case @PATH, or under script directory) or empty string if not found or executable
The function will execute 2 tests on the configuration file : presence and the fact that the file is readable.
parameters : $configuration_file, the configuration file to test
returns : 1 if tests were successful, 0 otherwise
Benjamin Grenier-Boley <benjamin.grenier-boley@inria.fr>