--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_2_1a/scripts/queue.pl	Fri Apr 20 14:47:09 2012 -0400
@@ -0,0 +1,127 @@
+#!/usr/bin/perl
+
+#-------------------------------------------------------------------------------
+# Simple queue management program
+# Attempts to keep 'numProc' processes running at the same time
+#
+# Proceses are defined in a file (one line per process)
+#
+# Every executed process creates two files: 'pid.stdout' and 'pid.stderr' where
+# pid is the process ID. The files contain STDOUT and STDERR for that process.
+#
+#																Pablo Cingolani
+#-------------------------------------------------------------------------------
+
+use strict;
+use POSIX;
+
+
+my($uptimeCmd) = "/usr/bin/uptime";		# Uptime command
+my($maxUptime);
+$| = 1;									# Don't use buffers for STDIN/STDOUT
+
+#-------------------------------------------------------------------------------
+# Should a new process be run?
+# Check some conditions before trying to run the next process
+#-------------------------------------------------------------------------------
+sub shouldRun() {
+	if( $maxUptime < 0 )	{ return 1; }	# Always true if $maxUptime is negative
+	my($utRes) = `$uptimeCmd`;
+	my($ut) = 0;
+	if( $utRes =~ /load average:\s+(\d+\.\d+),/ ) { $ut = $1; }
+	return $ut < $maxUptime;
+}
+
+#-------------------------------------------------------------------------------
+# Print something 'printLog' style
+#-------------------------------------------------------------------------------
+sub printLog($) {
+	my($str) = @_;
+	my($now) = strftime "%Y-%m-%d %H:%M:%S", localtime;
+	print "$now\t$str\n";
+}
+
+#-------------------------------------------------------------------------------
+# Main
+#-------------------------------------------------------------------------------
+# Usage: queue numProc File
+my($maxNumProc, $sleepTime, $file);
+($maxNumProc, $maxUptime, $sleepTime, $file) = @ARGV;
+if( $file eq '' ) {
+	print "Usage: queue.pl maxNumProc maxUptime sleepTime file\n";
+	print "Where:\n";
+	print "\tnumProc    Number of simultaneous processes\n";
+	print "\tmaxUptime  Maximum allowed uptime (otherwise, pause before launching the next process). Negative means don't care.\n";
+	print "\tsleepTime  Number of seconds to sleep after running a process (zero means no sleep)\n";
+	print "\tfile       File containing all commands to be executed (one per line)\n";
+	exit(10);
+}
+
+#---
+# Read file and launch processes
+#---
+my($cmd);
+my($startTime) = time();
+my($numProc) = 0;
+open BATCH, $file;
+while( $cmd = <BATCH> ) {
+	chomp $cmd;
+
+	# Can we launch more processes?
+	if( $numProc < $maxNumProc ) {
+
+		my( $run ) = 0;
+
+		do {	
+			 # Should the next process run now? (don't run if CPU is too high)
+			if( shouldRun() ) {
+				my $retFork = fork();
+				$run = 1;
+        
+				if( $retFork == 0 ) { # Child process
+					# Redirect STDOUT and STDERR to files
+					open STDOUT, '>', "$$.stdout" or die "Can't redirect STDOUT (PID=$$): $!";
+					open STDERR, '>', "$$.stderr" or die "Can't redirect STDERR (PID=$$): $!";
+					exec($cmd);
+				} elsif ($retFork == '' ) { # Error launching process
+					print STDERR "Error launching process:\t'$cmd'\n";
+				} else {
+					printLog("Executing (PID=$retFork):\t'$cmd'");
+					$numProc++;
+				}
+			} else { printLog("No running"); }
+                
+			# Sleep before next process
+			if( $sleepTime > 0 ) {
+				printLog "Sleep $sleepTime seconds";
+				sleep($sleepTime);
+			}
+		} while( ! $run );
+	} 
+
+	# Number of processes exceded? => Wait until one finishes
+	if( $numProc >= $maxNumProc ) {
+		# Wait for processes to die
+		my $deadPid = wait();
+		printLog "Process PID=$deadPid finished.";
+		$numProc--;
+		if( $numProc > 0 )	{ print "There " . ($numProc > 1 ? "are" : "is" ) . " still $numProc processes running.\n"; }
+	}
+}
+
+#---
+# Done, wait for the remining processes to die
+#---
+my($deadPid);
+while( ($deadPid = wait()) >= 0 ) { # Wait for processes to die
+	$numProc--;
+	my($now) = localtime();
+	printLog "Process PID=$deadPid finished.";
+	if( $numProc > 0 )	{ print "There " . ($numProc > 1 ? "are" : "is" ) . " still $numProc processes running.\n"; }
+}
+
+my($elapsed) = time() - $startTime;
+print "All processes finished.\nElapsed time $elapsed seconds.\n";
+
+close BATCH;
+