diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
index 944ef7977..60c9d9a59 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
@@ -28,7 +28,7 @@ import org.testng.annotations.Test
 import org.broadinstitute.sting.BaseTest
 
 class DataProcessingPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testSimpleBAM {
     val projectName = "test1"
     val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
@@ -45,7 +45,7 @@ class DataProcessingPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testBWAPEBAM {
     val projectName = "test2"
     val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
index 3e9af3e68..dd07cbfdc 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
@@ -28,7 +28,7 @@ import org.testng.annotations.Test
 import org.broadinstitute.sting.BaseTest
 
 class PacbioProcessingPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testPacbioProcessingPipeline {
     val testOut = "exampleBAM.recal.bam"
     val spec = new PipelineTestSpec
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
index 92c40acb1..6bc6b56db 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
@@ -53,7 +53,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class DevNullOutputPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testDevNullOutput() {
     val spec = new PipelineTestSpec
     spec.name = "devnulloutput"
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
index 9d885dda2..f52632a7f 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class ExampleCountLociPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testCountLoci() {
     val testOut = "count.out"
     val spec = new PipelineTestSpec
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
index 1b965d8d2..c23c12719 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class ExampleCountReadsPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testCountReads() {
     val spec = new PipelineTestSpec
     spec.name = "countreads"
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
index c6e4c3507..4ffaf7b5c 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
@@ -77,7 +77,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class ExampleReadFilterPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testExampleReadFilter() {
     val spec = new PipelineTestSpec
     spec.name = "examplereadfilter"
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
index a9a5928fc..0215a389c 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class ExampleRetryMemoryLimitPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testRetryMemoryLimit() {
     val spec = new PipelineTestSpec
     spec.name = "RetryMemoryLimit"
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala
index f6fcd7c12..67ac68c28 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
 
 class ExampleUnifiedGenotyperPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testUnifiedGenotyper() {
     val spec = new PipelineTestSpec
     spec.name = "unifiedgenotyper"
@@ -51,7 +51,7 @@ class ExampleUnifiedGenotyperPipelineTest {
       Array("vcf_intervals", BaseTest.validationDataLocation + "intervalTest.1.vcf")
     ).asInstanceOf[Array[Array[Object]]]
 
-  @Test(dataProvider = "ugIntervals")
+  @Test(dataProvider = "ugIntervals", timeOut=36000000)
   def testUnifiedGenotyperWithIntervals(intervalsName: String, intervalsPath: String) {
     val spec = new PipelineTestSpec
     spec.name = "unifiedgenotyper_with_" + intervalsName
@@ -64,7 +64,7 @@ class ExampleUnifiedGenotyperPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testUnifiedGenotyperNoGCOpt() {
     val spec = new PipelineTestSpec
     spec.name = "unifiedgenotyper_no_gc_opt"
@@ -80,7 +80,7 @@ class ExampleUnifiedGenotyperPipelineTest {
   @DataProvider(name="resMemReqParams")
   def getResMemReqParam = Array(Array("mem_free"), Array("virtual_free")).asInstanceOf[Array[Array[Object]]]
 
-  @Test(dataProvider = "resMemReqParams")
+  @Test(dataProvider = "resMemReqParams", timeOut=36000000)
   def testUnifiedGenotyperResMemReqParam(reqParam: String) {
     val spec = new PipelineTestSpec
     spec.name = "unifiedgenotyper_" + reqParam
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
index a43727ba6..50fc529dd 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
@@ -28,7 +28,7 @@ import org.testng.annotations.Test
 import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 
 class HelloWorldPipelineTest {
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorld() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorld"
@@ -37,7 +37,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithRunName() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithRunName"
@@ -47,7 +47,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithMemoryLimit() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldMemoryLimit"
@@ -57,7 +57,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithPriority() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithPriority"
@@ -67,7 +67,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithLsfResource() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithLsfResource"
@@ -77,7 +77,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithLsfResourceAndMemoryLimit() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithLsfResourceAndMemoryLimit"
@@ -87,7 +87,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithLsfEnvironment() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithLsfEnvironment"
@@ -97,7 +97,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithGridEngineResource() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithGridEngineResource"
@@ -107,7 +107,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithGridEngineResourceAndMemoryLimit() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithGridEngineResourceAndMemoryLimit"
@@ -117,7 +117,7 @@ class HelloWorldPipelineTest {
     PipelineTest.executeTest(spec)
   }
 
-  @Test
+  @Test(timeOut=36000000)
   def testHelloWorldWithGridEngineEnvironment() {
     val spec = new PipelineTestSpec
     spec.name = "HelloWorldWithGridEngineEnvironment"