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Top Forums UNIX for Dummies Questions & Answers Edit $args within a command Post 302924137 by gandolf989 on Thursday 6th of November 2014 12:47:25 PM
Old 11-06-2014
You may want to write a Perl wrapper with the YAML library. Perl and YAML are really good at reading configuration files. You would then have a configuration file with all of the parameters that you need to make the bowtie2 call, you can parse all of the inputs and more simply change the inputs to what you need and make it work. It would probably be easier to read and understand then the approach you are taking. etc..etc..

Here is the install page for YAML. I am using Perl and YAML to build a software installer. The customer will only need to provide the response file to make it work. Which is much easier than handling each parameter separately. And I can directly reference any parameter as $yaml_hash->{field_name}.

YAML - search.cpan.org
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YAML::Any(3)						User Contributed Perl Documentation					      YAML::Any(3)

NAME
YAML::Any - Pick a YAML implementation and use it. SYNOPSIS
use YAML::Any; $YAML::Indent = 3; my $yaml = Dump(@objects); DESCRIPTION
There are several YAML implementations that support the Dump/Load API. This module selects the best one available and uses it. ORDER
Currently, YAML::Any will choose the first one of these YAML implementations that is installed on your system: YAML::XS YAML::Syck YAML::Old YAML YAML::Tiny OPTIONS
If you specify an option like: $YAML::Indent = 4; And YAML::Any is using YAML::XS, it will use the proper variable: $YAML::XS::Indent. SUBROUTINES
Like all the YAML modules that YAML::Any uses, the following subroutines are exported by default: Dump Load and the following subroutines are exportable by request: DumpFile LoadFile METHODS
YAML::Any provides the following class methods. YAML::Any->order; This method returns a list of the current possible implementations that YAML::Any will search for. YAML::Any->implementation; This method returns the implementation the YAML::Any will use. This result is obtained by finding the first member of YAML::Any->order that is either already loaded in %INC or that can be loaded using "require". If no implementation is found, an error will be thrown. AUTHOR
Ingy doet Net <ingy@cpan.org> COPYRIGHT
Copyright (c) 2008. Ingy doet Net. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See <http://www.perl.com/perl/misc/Artistic.html> POD ERRORS
Hey! The above document had some coding errors, which are explained below: Around line 191: Non-ASCII character seen before =encoding in 'doet'. Assuming UTF-8 perl v5.16.3 2012-07-13 YAML::Any(3)
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