generate-settings

#!/usr/bin/env perl

use strict;
use warnings;
use File::Basename;

my $HELP = <<HELP;

  Generate the initial settings.txt file for a specified genome.

  usage: generate-settings genome
  * genome = name (hg19, mm10, etc.) or exact dir (contains genome.fa and genes.gtf)

HELP

if (!$ARGV[0]) {
	die $HELP;
}

main();

# main subroutine
sub main {
	my $genome_arg = $ARGV[0];

	# pipeline directory (the directory that this file is in)
	my $pipeline_dir = dirname(__FILE__);

	# settings file
	my $settings_file = "settings.txt";

	# set genome setting
	my $genome_dir_setting;
	if ($genome_arg =~ m/\//) {
		# use directory if given
		$genome_dir_setting = "GENOME-DIR|${genome_arg}\n";
	}
	else {
		# use id460 dir as reference if genome name is provided
		$genome_dir_setting = "GENOME-DIR|/ifs/home/id460/ref/${genome_arg}\n";
	}

	# save genome setting
	open(my $fh, ">", $settings_file);
	# print $fh $genome_setting;
	print $fh $genome_dir_setting;
	close $fh;

	# set fasta to test genome dir setting
	# system("bash ${pipeline_dir}/scripts/get-set-setting.sh $settings_file REF-FASTA");

	# get values to make sure they were set properly
	my $settings_genome = `bash ${pipeline_dir}/scripts/get-set-setting.sh $settings_file GENOME-DIR`;
	my $settings_fasta = `bash ${pipeline_dir}/scripts/get-set-setting.sh $settings_file REF-FASTA`;

	# print values
	print STDERR "\n";
	print STDERR " REF DIR : $settings_genome \n";
	print STDERR " REF FASTA : $settings_fasta \n";

}



# end