Bio::Tools::Run::AbstractRunner.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

Sommaire

NAME

Bio::Tools::Run::AbstractRunner

SYNOPSIS

*** Give standard usage here

DESCRIPTION

Objective

The problems of bioperl-run wrapper before the time this module is made are:
•
There are a lot of duplicate code among bioperl-run modules
•
It seems only to support object-in-object-out process, while sometimes people just need file-in-file-out one, which has been actually implemented but not exposed as a public method.
•
the different implementations, which should be similar and easy, confuse the new developers who wants to make wrappers for their own programs but did not know how. So it is better to review bioperl-run and make the simple things as they should be.

Temp file issues

     $runner->add_tmp_file($tmp_file);
     $runner->remove_tmp_files;

Unimplemented

Since it is an abstract module where there are methods to be implemented in the concrete modules
•
final_param
•
_find_files
•
_create_input_files
•
_parse_output_files

AUTHOR

Juguang Xiao, juguang at tll.org.sg This module is a free software. You may copy or redistribute it under the same terms as Perl itself.