diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index 202bc383d..88229e720 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -185,12 +185,14 @@
                 <configuration>
                     <!-- See explicit executions below -->
                     <skip>true</skip>
+                    <failIfNoTests>false</failIfNoTests>
+                    <!-- Pass various system properties -->
                     <systemPropertyVariables>
-                        <!-- TODO: Fix BaseTest to not error out if this property is missing. -->
-                        <pipeline.run>false</pipeline.run>
+                        <java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
                     </systemPropertyVariables>
                 </configuration>
                 <executions>
+                    <!-- Disable maven default execution -->
                     <execution>
                         <id>default-test</id>
                         <phase>none</phase>
@@ -218,9 +220,10 @@
                 <configuration>
                     <!-- See explicit executions below -->
                     <skip>true</skip>
+                    <failIfNoTests>false</failIfNoTests>
+                    <!-- Pass various system properties -->
                     <systemPropertyVariables>
-                        <!-- TODO: Fix BaseTest to not error out if this property is missing. -->
-                        <pipeline.run>false</pipeline.run>
+                        <java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
                     </systemPropertyVariables>
                 </configuration>
                 <executions>
diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java
index 9ceb5904d..e8aed7d50 100644
--- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java
+++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java
@@ -135,7 +135,7 @@ public abstract class BaseTest {
     public final static String NA12878_PCRFREE = privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam";
     public final static String NA12878_WEx = privateTestDir + "CEUTrio.HiSeq.WEx.b37_decoy.NA12878.20_10_11mb.bam";
 
-    public static final boolean pipelineTestRunModeIsSet = System.getProperty("pipeline.run").equals("run");
+    public static final boolean pipelineTestRunModeIsSet = System.getProperty("pipeline.run", "").equals("run");
 
     /** before the class starts up */
     static {
diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml
index 1f384427e..a57beefde 100644
--- a/public/sting-root/pom.xml
+++ b/public/sting-root/pom.xml
@@ -359,8 +359,6 @@
                         <systemPropertyVariables>
                             <clover.pertest.coverage>diff</clover.pertest.coverage>
                             <java.awt.headless>true</java.awt.headless>
-                            <!-- TODO: Fix BaseTest to not error out if this property is missing. -->
-                            <pipeline.run>${sting.pipelinetests.run}</pipeline.run>
                             <java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
                         </systemPropertyVariables>
                     </configuration>