#!/usr/bin/perl

# load modules
use Getopt::Std;

##########################
# COMMAND LINE ARGUMENTS #
##########################
# u = (u)ser email from galaxy
# s = subject
# a = sample (a)nnotation
# g = sample (g)ender
# o = (o)utput file (simple text file)
getopts('u:s:o:d:', \%opts);  # option are in %opts


if (!exists($opts{'u'})) {
	die('no email specified');
}
$email = $opts{'u'};

if (exists($opts{'s'}) && $opts{'s'} ne '') {
	$subject = $opts{'s'};
}
else {
	$subject = "Galaxy Workflow or Job Finished\n";
}

# first compose message.
open OUT, ">mail.txt";
print OUT "to: $email\n";
print OUT "subject: $subject\n";
## EDIT THE FROM EMAIL !!!
print OUT "from: ADMIN\@Your.Galaxy.org\n\n";
print OUT "Your Workflow on the Biomina Galaxy instance is finished. \n\n";
#print OUT "Access the results at : http://143.169.238.104/galaxy/\n";
if (exists($opts{'d'})) {
	my @files = split(/@@@/,$opts{'d'});
	print OUT "\n\nThe following datasets needed to be available before sending this notice:\n";
	foreach (@files) {
		$_ =~ s/^\s+//;
		if ($_ eq '') {
			next;
		}
		print OUT " - $_\n";
	}
}
print OUT "\n\nPlease clean up unneeded datafiles, including hidden files (select 'show hidden').\n";
close OUT;
system("sendmail $email < mail.txt");
system("rm -f mail.txt");