From 6185e8c43255d7213f4d4c464c71ff3b5e1a09d4 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Thu, 1 Nov 2012 17:48:58 -0400
Subject: [PATCH] Allow large-scale tests 5 hours each to run

---
 .../walkers/genotyper/UnifiedGenotyperLargeScaleTest.java   | 6 +++---
 .../gatk/walkers/indels/IndelRealignerLargeScaleTest.java   | 4 ++--
 .../indels/RealignerTargetCreatorLargeScaleTest.java        | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java
index 109088875..c5a5dcc21 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java
@@ -7,7 +7,7 @@ import java.util.ArrayList;
 
 public class UnifiedGenotyperLargeScaleTest extends WalkerTest {
 
-    @Test
+    @Test( timeOut = 18000000 )
     public void testUnifiedGenotyperWholeGenome() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-R " + hg18Reference +
@@ -22,7 +22,7 @@ public class UnifiedGenotyperLargeScaleTest extends WalkerTest {
         executeTest("testUnifiedGenotyperWholeGenome", spec);
     }
 
-    @Test
+    @Test( timeOut = 18000000 )
     public void testUnifiedGenotyperWholeExome() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-R " + hg18Reference +
@@ -37,7 +37,7 @@ public class UnifiedGenotyperLargeScaleTest extends WalkerTest {
         executeTest("testUnifiedGenotyperWholeExome", spec);
     }
 
-    @Test
+    @Test( timeOut = 18000000 )
     public void testUnifiedGenotyperWGParallel() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-R " + hg18Reference +
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java
index 4526fc0d7..2dd5a66fd 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java
@@ -6,7 +6,7 @@ import org.testng.annotations.Test;
 import java.util.ArrayList;
 
 public class IndelRealignerLargeScaleTest extends WalkerTest {
-    @Test
+    @Test( timeOut = 18000000 )
     public void testHighCoverage() {
         WalkerTestSpec spec = new WalkerTestSpec(
 
@@ -21,7 +21,7 @@ public class IndelRealignerLargeScaleTest extends WalkerTest {
         executeTest("testIndelRealignerHighCoverage", spec);
     }
 
-    @Test
+    @Test( timeOut = 18000000 )
     public void testRealigner() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java
index 3203ee100..e32afd06b 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java
@@ -6,7 +6,7 @@ import org.testng.annotations.Test;
 import java.util.ArrayList;
 
 public class RealignerTargetCreatorLargeScaleTest extends WalkerTest {
-    @Test
+    @Test( timeOut = 18000000 )
     public void testRealignerTargetCreator() {
 
         WalkerTestSpec spec1 = new WalkerTestSpec(