Start delivery code

	close($complete_handle);

};

$possible_actions{deliver} = sub {

	# Get the run folder from the command line

	# (Same as with the `run` action)

	if (scalar(@ARGV) < 1) {

		log_msg(<<"EOL");

When using the `run` action, please provide the path to the run folder.

For example: $RealScript run 160804-NS500126-0555-ABCDEFG

EOL

		exit 1;

	}

	my $candidate_runfolder = shift @ARGV;

	# Make sure the run folder is valid, and also set $RUNFOLDER

	# (Same as with the `run` action)

	$RUNFOLDER = validate_path($candidate_runfolder);

	if (!defined($RUNFOLDER)) {

		log_msg(<<"EOL");

The run folder you provided does not exist, is not a directory, or cannot be

read.  Please re-run your command with a valid folder path.

The path you provided is: $candidate_runfolder

EOL

		exit 1;

	}

	# Let's also set $SEARCHFOLDER, $LOGPATH, and $LOCKPATH

	# (Same as with the `run` action)

	$SEARCHFOLDER = Cwd::abs_path("$RUNFOLDER/../..");

	$LOGPATH = "$RUNFOLDER/workflow-log.txt";

	$LOCKPATH = "$RUNFOLDER/workflow-lock.txt";

	# Get a lock on our run folder

	# (Same as with the `run` action)

	lock_get() or exit(1);

	# Start logging to file

	# (Same as with the `run` action)

	log_open() or exit(1);

	# Search for Project_ directories

	my $basecalls_path = "$RUNFOLDER/Data/Intensities/BaseCalls";

	my $basecalls_handle;

	my @candidate_projects;

	log_msg("Searching for Project directories...\n");

	opendir($basecalls_handle, $basecalls_path) or do {

		log_msg(<<"EOF");

We had a problem accessing the BaseCalls directory.

The path we tried to access is: $basecalls_path

The error we got is: $!

EOF

		exit(1);

	};

	while (my $project_name = readdir($basecalls_handle)) {

		if ($project_name !~ m{\AProject_[a-z0-9]+\z}xims) {

			log_msg("$project_name doesn't look like a Project.  ");

			log_msg("Skipping...\n");

		}

		log_msg("Found Project directory $project_name\n");

		push @candidate_projects, $project_name;

	}

	# Exit if we don't find any Project directories

	if (!scalar(@candidate_projects)) {

		log_msg(<<"EOF");

We could not find any Project directories.

The run folder we were searching is: $RUNFOLDER

Please make sure that an analysis was completed, and try your command again.

EOF

		return;

	}

	# Now, perform the delivery on each candidate project

	foreach my $project (@candidate_projects) {

		deliver($SEARCHFOLDER, $RUNFOLDER, $project,

		        "$RealBin/email-recipients.txt", $LOGPATH);

	}

	log_msg("Delivery complete!\n");

	return;

};

# Now that we have our actions, let's execute the code

if (exists($possible_actions{$ACTION})) {

	# We are getting a subroutine reference from a Perl hash, dereferencing

# 

# Deliver files for a given project

# $runfolder The path to the run folder.

# $project: The name of the Project path.

# $email: The email-recipients.txt config file.

# $log: The path to the log file

sub deliver {

	my ($runfolder, $project, $email, $log) = @_;

	log_msg("Starting delivery for $project\n");

	# Extract the username

	$project =~ m{\AProject_(.+)\z}xims;

	my $username = $1;

	# Search for any home directories matching this username

	# We have a hard-coded exceptin for user "spyros"

	my @homedirs;

	if ($username eq 'spyros') {

		@homedirs = ('/b7_1/home/spyros');

	} else {

		@homedirs = glob "/b?_?/home*/$username";

	}

	# If we don't find anything, send an email and return

	if (!scalar(@homedirs)) {

		log_msg("No home directory found for $username!\n");

		return 1;

	}

	# Now, let's get to work

	log_msg("Will do delivery to user $username\n");

	# All done!

	return 1;

}

# Given a runfolder, return the path to the laneBarcode.html file

sub barcode_path {

	my ($runfolder) = @_;