diff --git a/perl/runPipelineSanityCheck.pl b/perl/runPipelineSanityCheck.pl
new file mode 100755
index 000000000..6c2a3c382
--- /dev/null
+++ b/perl/runPipelineSanityCheck.pl
@@ -0,0 +1,177 @@
+#!/usr/bin/perl -w
+
+use strict;
+use Getopt::Long;
+use Data::Dumper;
+use File::Path;
+
+my @log;
+
+sub getTimestamp {
+    my ($sec, $min, $hour, $mday, $mon, $year, $wday, $yday, $isdst) = localtime(time);
+    my $timestamp = sprintf("%04d.%02d.%02d", 1900 + $year, $mon, $mday);
+
+    return $timestamp;
+}
+
+sub log {
+    my ($message) = @_;
+
+    my ($sec, $min, $hour, $mday, $mon, $year, $wday, $yday, $isdst) = localtime(time);
+    my $timestamp = sprintf("[%04d.%02d.%02d %02d:%02d:%02d]", 1900 + $year, $mon, $mday, $hour, $min, $sec);
+
+    my @message = split(/\n/, $message);
+    for (my $i = 0; $i <= $#message; $i++) {
+        $message[$i] = "$timestamp $message[$i]";
+    }
+
+    print STDOUT join("\n", @message) . "\n";
+
+    push(@log, @message);
+}
+
+sub emailLog {
+    my ($subject, $logfile, $email) = @_;
+
+    my $cmd = "mail -s '$subject' $email < $logfile";
+    system($cmd);
+}
+
+sub killPipeline {
+    chomp(my @jobs = qx(bjobs -P QueuePipelineTest));
+
+    my @ids;
+    foreach my $job (@jobs) {
+        if ($job =~ /^(\d+)\s+/) {
+            push(@ids, $1);
+        }
+    }
+
+    system("bkill " . join(" ", @ids));
+}
+
+sub execute {
+    my ($command, $output, $timeout, $run, $logfile, $email) = @_;
+
+    my $status = 0;
+    my $result = "(output not generated in dry-run mode)";
+
+    &log("Execute: '$command'");
+
+    if ($run == 1) {
+        eval {
+            local $SIG{'ALRM'} = sub { die("alarm\n") };
+            alarm($timeout);
+
+            $result = qx($command 2>&1);
+            $status = $?;
+
+            alarm(0);
+        };
+
+        if ($@) {
+            &log("Timeout: '$command' did not return within '$timeout' seconds");
+
+            if ($run == 1) {
+                open(LOG, ">$logfile");
+                print LOG join("\n", @log);
+                close(LOG);
+
+                &emailLog("Analysis pipeline nightly test: failed", $logfile, $email);
+                &killPipeline();
+            }
+
+            exit($status);
+        }
+    }
+
+    if ($status == 0) {
+        if ($output == 0) {
+            &log("Success: '$command' exited with code '$status'");
+        } else {
+            &log("Success: '$command' exited with code '$status'  Output:");
+            &log($result);
+        }
+
+        return 0;
+    }
+
+    &log("Failure: '$command' exited with code '$status'  Output:");
+
+    if (!defined($result)) {
+        $result = "(unable to capture)\n";
+    }
+
+    &log($result);
+
+    if ($run == 1) {
+        open(LOG, ">$logfile");
+        print LOG join("\n", @log);
+        close(LOG);
+
+        &emailLog("Analysis pipeline nightly test: failed", $logfile, $email);
+        &killPipeline();
+    }
+
+    exit($status);
+}
+
+# Default arguments
+my %args = (
+    'pipelineRoot' => "/humgen/gsa-hpprojects/analysis/pipeline",
+    'outputRoot' => "/humgen/gsa-hpprojects/analysis/pipeline/projects/QueuePipelineNightlyTest",
+    'testRepositoryDir' => "/humgen/gsa-hpprojects/analysis/pipeline/repositories/StingTest",
+    'testInputYAML' => "/humgen/gsa-hpprojects/GATK/data/Validation_Data/QueuePipelineTestData/QueuePipelineTestData.yaml",
+    'email' => "$ENV{'USER'}\@broadinstitute.org",
+    'run' => 0,
+);
+
+# Get command-line options
+GetOptions(
+    'outputRoot=s' => \$args{'outputRoot'},
+    'pipelineRoot=s' => \$args{'pipelineRoot'},
+    'testRepositoryDir=s' => \$args{'testRepositoryDir'},
+    'testInputYAML=s' => \$args{'testInputYAML'},
+    'email=s' => \$args{'email'},
+    'run' => \$args{'run'},
+    'help|h' => \$args{'help'}
+);
+
+# Should we emit some help?
+if ($args{'help'}) {
+    print Dumper(\%args) . "\n";
+    exit(0);
+}
+
+# Set some directories
+$args{'testDir'} = "$args{'outputRoot'}/" . &getTimestamp();
+$args{'testOutputDir'} = "$args{'testDir'}/output";
+$args{'logFile'} = "$args{'testDir'}/output.log";
+
+# Set up environment
+$ENV{'PATH'} = "$args{'testRepositoryDir'}/shell:$args{'testRepositoryDir'}/python:$ENV{'PATH'}";
+
+# Execute jobs
+&execute("echo \$PATH",                     1, 10, $args{'run'}, $args{'logFile'}, $args{'email'});
+&execute("mkdir -p $args{'testDir'}",       0, 10, $args{'run'}, $args{'logFile'}, $args{'email'});
+&execute("mkdir -p $args{'testOutputDir'}", 0, 10, $args{'run'}, $args{'logFile'}, $args{'email'});
+&execute("rm -rf $args{'logFile'}",         0, 10, $args{'run'}, $args{'logFile'}, $args{'email'});
+
+&execute("cd $args{'testRepositoryDir'} && svn cleanup",                        0, 120,  $args{'run'}, $args{'logFile'}, $args{'email'});
+&execute("cd $args{'testRepositoryDir'} && svn up",                             0, 600,  $args{'run'}, $args{'logFile'}, $args{'email'});
+&execute("cd $args{'testRepositoryDir'} && ant clean",                          0, 600,  $args{'run'}, $args{'logFile'}, $args{'email'});
+&execute("cd $args{'testRepositoryDir'} && ant dist playground oneoffs queue",  0, 1200, $args{'run'}, $args{'logFile'}, $args{'email'});
+&execute("cd $args{'testRepositoryDir'} && svn info",                           1, 10,   $args{'run'}, $args{'logFile'}, $args{'email'});
+
+&execute("cd $args{'testOutputDir'} && java -jar $args{'testRepositoryDir'}/dist/Queue.jar -jobProject QueuePipelineTest -S $args{'testRepositoryDir'}/scala/qscript/fullCallingPipeline.q -Y $args{'testInputYAML'} -refseqTable /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg18.txt --gatkjar $args{'testRepositoryDir'}/dist/GenomeAnalysisTK.jar -contigIntervals /humgen/gsa-hpprojects/analysis/pipeline/resources/whole_genome.intervals -titv 3.0 -skipCleaning -bsub -bsubWait", 0, 120, $args{'run'}, $args{'logFile'}, $args{'email'});
+&execute("cd $args{'testOutputDir'} && java -jar $args{'testRepositoryDir'}/dist/Queue.jar -jobProject QueuePipelineTest -S $args{'testRepositoryDir'}/scala/qscript/fullCallingPipeline.q -Y $args{'testInputYAML'} -refseqTable /humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg18.txt --gatkjar $args{'testRepositoryDir'}/dist/GenomeAnalysisTK.jar -contigIntervals /humgen/gsa-hpprojects/analysis/pipeline/resources/whole_genome.intervals -titv 3.0 -skipCleaning -bsub -bsubWait -run", 0, 1200, $args{'run'}, $args{'logFile'}, $args{'email'});
+
+&log("All tests completed successfully");
+
+if ($args{'run'} == 1) {
+    open(LOG, ">$args{'logFile'}");
+    print LOG join("\n", @log);
+    close(LOG);
+
+    &emailLog("Analysis pipeline nightly test: succeeded", $args{'logFile'}, $args{'email'});
+}