NAME
Smash::Analyses - Base class for analyses modules in Smash. Provides common functions used by many subclasses.
SYNOPSIS
An instance of this class is almost never created. This is sort-of an abstract class with definitions of some functions used by all its subclasses.
DESCRIPTION
Smash::Analyses is an abstract subclass of Smash::Core. It provides a set of common functions for its subclass.
KNOWN SUBCLASSES
Smash::Analyses::Assembler, Smash::Analyses::GenePredictor, Smash::Analyses::GenePredictorWrapper.
FUNCTIONS
General functions
- name
- Name of the instance. This should not to be confused with the name of the software represented by software_name which in turn calls the string overload of the object, or by predictor or assembler. This is used to identify the current run of the analysis software. All output files generated by this instance will be identified using this name.
- type
- type of object (Assembler, GenePredictor, etc)
- output_dir
- Output directory for this instance of the subclass of Smash::Analyses.
Software package related functions
- init_software_details
- This is a very crucial function in running an analysis software using Smash. It is called by Smash::Analyses when it (or any of its subclasses) is initialized. It looks for the requested version of the software for the current host and if it succeeds, then Smash knows where to find it. See "Finding the right software" in UserManual for details on how this works.
- software_name
- name of the analysis software, e.g. GeneMark
- version
- version of the software used by this instance
- pkg_dir
- location of the analysis software files
