templates.pl

#!perl
use strict;
use warnings;

use Template;

my $vars = {
	GENOME_BUILD_NAME => 'GENOME_BUILD_NAME_val',
	CHROMOSOME        => 'CHROMOSOME_val',
	SAMPLE_HASH       => {
		pairs => {
			123 => {
				sample_name => 'name123',
				bigwig_URL => 'url123',
			},
			234 => {
				sample_name => 'name234',
				bigwig_URL => 'url234',
			},
		},
	},
};

my $tt = Template->new();
$tt->process(\*DATA, $vars);

=sample output
track db=GENOME_BUILD_NAME_val position=CHROMOSOME_val type=bigWig name=name123 visibility=full bigDataUrl=url123
track db=GENOME_BUILD_NAME_val position=CHROMOSOME_val type=bigWig name=name234 visibility=full bigDataUrl=url234
=cut

__DATA__
[%- FOREACH library_pair IN SAMPLE_HASH.pairs %]
track db=[% GENOME_BUILD_NAME %] position=[% CHROMOSOME %] type=bigWig name=[% library_pair.value.sample_name %] visibility=full bigDataUrl=[% library_pair.value.bigwig_URL %]
[%- END %]