From 3848159086bfc6d3f1d1db199d7174b56a5c0c81 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Thu, 6 Feb 2014 01:17:26 +0800
Subject: [PATCH] Added a set of serial tests to gatk/queue packages, which
 runs all tests under their package in one TestNG execution. New properties to
 disable regenerating example resources artifact when each parallel test runs
 under packagetest. Moved collection of packagetest parameters from shell
 scripts into maven profiles. Fixed necessity of test-utils jar by removing
 incorrect dependenciesToScan element during packagetests. When building
 picard libraries, run clean first. Fixed tools jar dependency in picard pom.
 Integration tests properly use the ant-bridge.sh test.debug.port variable,
 like unit tests.

---
 ant-bridge.sh                                 | 11 +--
 pom.xml                                       | 92 +++++++++++------
 protected/gatk-protected/pom.xml              | 10 --
 public/external-example/pom.xml               | 18 ----
 public/gatk-framework/pom.xml                 | 20 +---
 public/gatk-package/pom.xml                   | 98 +++++++++++++++++++
 public/gsalib/pom.xml                         |  2 +-
 public/package-tests/pom.xml                  | 25 +++--
 public/queue-framework/pom.xml                |  4 +-
 public/queue-package/pom.xml                  | 97 ++++++++++++++++++
 .../picard/1.107.1676/picard-1.107.1676.pom   |  4 +-
 public/sting-utils/pom.xml                    |  1 -
 12 files changed, 284 insertions(+), 98 deletions(-)

diff --git a/ant-bridge.sh b/ant-bridge.sh
index e76e03930..860b3ecc5 100755
--- a/ant-bridge.sh
+++ b/ant-bridge.sh
@@ -33,6 +33,7 @@ for arg in "${@}" ; do
 
         elif [[ "${property_name}" == "test.debug.port" ]] ; then
             mvn_properties="${mvn_properties} -Dmaven.surefire.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
+            mvn_properties="${mvn_properties} -Dmaven.failsafe.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
 
         elif [[ "${property_name}" == "test.default.maxmemory" ]] ; then
             mvn_properties="${mvn_properties} -Dtest.maxmemory=${property_value}"
@@ -98,18 +99,16 @@ for arg in "${@}" ; do
         elif [[ "${arg}" == "gatkfull.binary.release.tests" ]] ; then
             local_repo="sitetemprepo"
             mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
-            mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
-            mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
-            mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
+            mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
+            mvn_args="${mvn_args} -Dsting.packagetests.enabled=true"
             mvn_args="${mvn_args} -Dsting.packagecommittests.skipped=false"
 
         # TODO: This runs only the pipeline tests (full, non-dry run), but not the commit tests for Queue.
         elif [[ "${arg}" == "queuefull.binary.release.tests" ]] ; then
             local_repo="sitetemprepo"
             mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
-            mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
-            mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
-            mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
+            mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
+            mvn_args="${mvn_args} -Dsting.packagetests.enabled=true"
             mvn_args="${mvn_args} -Dsting.packagepipelinetests.skipped=false"
             mvn_args="${mvn_args} -Dsting.pipelinetests.run=true"
 
diff --git a/pom.xml b/pom.xml
index 60b19f1b2..aef2baab3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -32,13 +32,37 @@
         <resource.bundle.skip>false</resource.bundle.skip>
         <!-- TODO: Need a better a way to say "don't include hidden" by default -->
         <gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
+
+        <!--
+        Phases of the build that may be disabled to speed up compilation.
+        -->
         <sting.jar.phase>package</sting.jar.phase>
-        <sting.test-utils.jar.phase>none</sting.test-utils.jar.phase>
+        <sting.generate-resources.phase>generate-resources</sting.generate-resources.phase>
+        <sting.process-resources.phase>process-resources</sting.process-resources.phase>
+        <sting.process-test-resources.phase>process-test-resources</sting.process-test-resources.phase>
+
+        <!--
+        Package tests ensure the consistency of the packaged / shaded jars.
+        It runs the tests where the monolithic jar is the only dependency on the classpath.
+        -->
         <sting.packagecommittests.skipped>true</sting.packagecommittests.skipped>
         <sting.packageunittests.skipped>${sting.packagecommittests.skipped}</sting.packageunittests.skipped>
         <sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
         <sting.packagepipelinetests.skipped>${sting.packagecommittests.skipped}</sting.packagepipelinetests.skipped>
         <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
+
+        <!--
+        Serial tests use the test jars to run tests, such that all tests are run from a single TestNG invocation.
+        This is different that the invoker, that runs the test classes from the filesystem, but pointing at the packaged JAR files.
+        TODO: Currently, all tests run within each package, since packages already collect dependencies for shading an uber jar.
+        TODO: Should there be another level up of tests, possibly running "all tests" via this aggregator level?
+        TODO: If that require the aggregator to be dependent on the child dependencies, perhaps a better approach might be another monolithic test project.
+        -->
+        <sting.serialcommittests.skipped>true</sting.serialcommittests.skipped>
+        <sting.serialunittests.skipped>${sting.serialcommittests.skipped}</sting.serialunittests.skipped>
+        <sting.serialintegrationtests.skipped>${sting.serialcommittests.skipped}</sting.serialintegrationtests.skipped>
+        <sting.serialpipelinetests.skipped>${sting.serialcommittests.skipped}</sting.serialpipelinetests.skipped>
+        <sting.seriallargescaletests.skipped>true</sting.seriallargescaletests.skipped>
     </properties>
 
     <dependencies>
@@ -109,6 +133,20 @@
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-resources-plugin</artifactId>
                     <executions>
+                        <execution>
+                            <id>default-resources</id>
+                            <goals>
+                                <goal>resources</goal>
+                            </goals>
+                            <phase>${sting.process-resources.phase}</phase>
+                        </execution>
+                        <execution>
+                            <id>default-testResources</id>
+                            <goals>
+                                <goal>testResources</goal>
+                            </goals>
+                            <phase>${sting.process-test-resources.phase}</phase>
+                        </execution>
                         <execution>
                             <id>copy-resource-bundle-log4j</id>
                             <goals>
@@ -277,38 +315,13 @@
                             <phase>${sting.jar.phase}</phase>
                         </execution>
                         <execution>
-                            <id>test-utils</id>
+                            <id>test-jar</id>
                             <goals>
-                                <goal>jar</goal>
+                                <goal>test-jar</goal>
                             </goals>
-                            <phase>${sting.test-utils-jar.phase}</phase>
+                            <phase>${sting.jar.phase}</phase>
                             <configuration>
-                                <classesDirectory>${project.build.testOutputDirectory}</classesDirectory>
-                                <classifier>test-utils</classifier>
-                                <!--
-                                TODO: Excluding actual tests from tests-utils jar is required because the same test classes
-                                TODO: cannot be in both the test artifact AND the test classes directory.
-
-                                TODO: Otherwise maven throws an [ERROR] java.lang.RuntimeException: Duplicate test set
-
-                                TODO: This is due to AbstractSurefireMojo.scanForTestClasses() adding both scanDirectories() and scanDependencies().
-                                TODO: Pain to debug as exception is three maven invoker levels deep, outer maven, maven-inovker-plugin, then forked tests!
-
-                                TODO: See also: http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
-
-                                TODO: Then that dependency won't have test classes that will also run from the
-                                TODO: test classes directory during the invoked package test.
-                                -->
-                                <excludes>
-                                    <exclude>**/*UnitTest.class</exclude>
-                                    <exclude>**/*UnitTest$*.class</exclude>
-                                    <exclude>**/*IntegrationTest.class</exclude>
-                                    <exclude>**/*IntegrationTest$*.class</exclude>
-                                    <exclude>**/*PipelineTest.class</exclude>
-                                    <exclude>**/*PipelineTest$*.class</exclude>
-                                    <exclude>**/*LargeScaleTest.class</exclude>
-                                    <exclude>**/*LargeScaleTest.class</exclude>
-                                </excludes>
+                                <skipIfEmpty>true</skipIfEmpty>
                             </configuration>
                         </execution>
                     </executions>
@@ -773,6 +786,25 @@
                 <module>private</module>
             </modules>
         </profile>
+
+        <!-- Collection of properties for use during package testing -->
+        <profile>
+            <id>packagetests-enabled</id>
+            <activation>
+                <property>
+                    <name>sting.packagetests.enabled</name>
+                    <value>true</value>
+                </property>
+            </activation>
+            <properties>
+                <maven.javadoc.skip>true</maven.javadoc.skip>
+                <sting.generate-gatk-extensions.skipped>true</sting.generate-gatk-extensions.skipped>
+                <sting.jar.phase>none</sting.jar.phase>
+                <sting.generate-resources.phase>none</sting.generate-resources.phase>
+                <sting.process-resources.phase>none</sting.process-resources.phase>
+                <sting.process-test-resources.phase>none</sting.process-test-resources.phase>
+            </properties>
+        </profile>
     </profiles>
 
 </project>
diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-protected/pom.xml
index c0074b8bc..9fcd6f6cf 100644
--- a/protected/gatk-protected/pom.xml
+++ b/protected/gatk-protected/pom.xml
@@ -40,20 +40,10 @@
             <artifactId>fastutil</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>sting-utils</artifactId>
-            <version>${project.version}</version>
-            <classifier>test-utils</classifier>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
-
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
-            <classifier>test-utils</classifier>
             <type>test-jar</type>
             <scope>test</scope>
         </dependency>
diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index 0f5e3934e..299216cc2 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -38,27 +38,10 @@
             <version>${sting.version}</version>
         </dependency>
 
-        <!--
-        Test dependencies are not transitive,
-        so must include each explicit test artifact.
-
-        TODO: switch from test-utils classifier to a tests-utils artifact
-        TODO: see also http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
-        -->
-        <dependency>
-            <groupId>org.broadinstitute.sting</groupId>
-            <artifactId>sting-utils</artifactId>
-            <version>${sting.version}</version>
-            <classifier>test-utils</classifier>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
-
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${sting.version}</version>
-            <classifier>test-utils</classifier>
             <type>test-jar</type>
             <scope>test</scope>
         </dependency>
@@ -208,7 +191,6 @@
                         <phase>none</phase>
                     </execution>
                     <execution>
-                        <!-- run all non integration tests -->
                         <id>unit-tests</id>
                         <goals>
                             <goal>test</goal>
diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml
index bf46e8951..956cf693a 100644
--- a/public/gatk-framework/pom.xml
+++ b/public/gatk-framework/pom.xml
@@ -16,7 +16,6 @@
     <properties>
         <sting.basedir>${project.basedir}/../..</sting.basedir>
         <sting.packagetests.artifactId>gatk-package</sting.packagetests.artifactId>
-        <sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
     </properties>
 
     <dependencies>
@@ -26,15 +25,6 @@
             <version>${project.version}</version>
         </dependency>
 
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>sting-utils</artifactId>
-            <version>${project.version}</version>
-            <classifier>test-utils</classifier>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
-
         <dependency>
             <groupId>org.testng</groupId>
             <artifactId>testng</artifactId>
@@ -55,7 +45,7 @@
                 <executions>
                     <execution>
                         <id>example-resources</id>
-                        <phase>generate-resources</phase>
+                        <phase>${sting.generate-resources.phase}</phase>
                     </execution>
                 </executions>
             </plugin>
@@ -79,14 +69,6 @@
                     </execution>
                 </executions>
             </plugin>
-            <!--
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <executions>
-                </executions>
-            </plugin>
--->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-invoker-plugin</artifactId>
diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml
index 48c6168d3..0ff69b047 100644
--- a/public/gatk-package/pom.xml
+++ b/public/gatk-package/pom.xml
@@ -51,10 +51,79 @@
             <classifier>example-resources</classifier>
             <type>tar.bz2</type>
         </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.google.caliper</groupId>
+            <artifactId>caliper</artifactId>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>unit-tests</id>
+                        <configuration>
+                            <skip>${sting.serialunittests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-failsafe-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>integration-tests</id>
+                        <configuration>
+                            <skip>${sting.serialintegrationtests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>pipeline-tests</id>
+                        <configuration>
+                            <skip>${sting.serialpipelinetests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>large-scale-tests</id>
+                        <configuration>
+                            <skip>${sting.seriallargescaletests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-dependency-plugin</artifactId>
@@ -132,6 +201,14 @@
                     <version>${project.version}</version>
                     <optional>true</optional>
                 </dependency>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>gatk-protected</artifactId>
+                    <version>${project.version}</version>
+                    <type>test-jar</type>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
             </dependencies>
         </profile>
         <profile>
@@ -148,8 +225,29 @@
                     <version>${project.version}</version>
                     <optional>true</optional>
                 </dependency>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>gatk-private</artifactId>
+                    <version>${project.version}</version>
+                    <type>test-jar</type>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
             </dependencies>
         </profile>
+        <profile>
+            <id>packagetests-enabled</id>
+            <activation>
+                <property>
+                    <name>sting.packagetests.enabled</name>
+                    <value>true</value>
+                </property>
+            </activation>
+            <properties>
+                <sting.unpack.phase>none</sting.unpack.phase>
+                <sting.shade.phase>none</sting.shade.phase>
+            </properties>
+        </profile>
     </profiles>
 
 </project>
diff --git a/public/gsalib/pom.xml b/public/gsalib/pom.xml
index c751bc0f0..66845f584 100644
--- a/public/gsalib/pom.xml
+++ b/public/gsalib/pom.xml
@@ -30,7 +30,7 @@
                         <goals>
                             <goal>single</goal>
                         </goals>
-                        <phase>generate-resources</phase>
+                        <phase>${sting.generate-resources.phase}</phase>
                         <configuration>
                             <appendAssemblyId>false</appendAssemblyId>
                             <descriptors>
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index 62a1d570b..8b7c4e7f7 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -48,13 +48,29 @@
             <artifactId>cofoja</artifactId>
         </dependency>
 
+        <!--
+        gatk-framework test-jar added for BaseTest
+        TODO: Uncomment below to use the explicitly bad "exclude *" to really test correct packaging,
+        TODO: until we can separate BaseTest and other utilities into their own sting-test-utils artifact.
+        TODO: We only want the classes in the packaged jars tested, not the classes within the dependency jars too.
+        See also:
+          http://stackoverflow.com/questions/547805/how-to-exclude-all-transitive-dependencies-of-a-maven-dependency
+          http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
+        -->
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
-            <classifier>test-utils</classifier>
             <type>test-jar</type>
             <scope>test</scope>
+            <!--
+            <exclusions>
+                <exclusion>
+                    <groupId>*</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+            </exclusions>
+            -->
         </dependency>
 
         <dependency>
@@ -95,13 +111,9 @@
                             <workingDirectory>${sting.packagetests.basedir}</workingDirectory>
                             <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
                             <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
-                            <dependenciesToScan>
-                                <scan>org.broadinstitute.sting:.*</scan>
-                            </dependenciesToScan>
                         </configuration>
                         <executions>
                             <execution>
-                                <!-- run all non integration tests -->
                                 <id>unit-tests</id>
                                 <goals>
                                     <goal>test</goal>
@@ -137,9 +149,6 @@
                             <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
                             <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
                             <summaryFile>${failsafe.summaryFile}</summaryFile>
-                            <dependenciesToScan>
-                                <scan>org.broadinstitute.sting:.*</scan>
-                            </dependenciesToScan>
                         </configuration>
                         <executions>
                             <execution>
diff --git a/public/queue-framework/pom.xml b/public/queue-framework/pom.xml
index 7146e9694..7a292ffe4 100644
--- a/public/queue-framework/pom.xml
+++ b/public/queue-framework/pom.xml
@@ -18,7 +18,6 @@
         <gatk.extensions.sources>${project.build.directory}/generated-sources/gatk-extensions</gatk.extensions.sources>
         <sting.generate-gatk-extensions.skipped>false</sting.generate-gatk-extensions.skipped>
         <sting.packagetests.artifactId>queue-package</sting.packagetests.artifactId>
-        <sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
     </properties>
 
     <dependencies>
@@ -66,7 +65,6 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
-            <classifier>test-utils</classifier>
             <type>test-jar</type>
             <scope>test</scope>
         </dependency>
@@ -130,7 +128,7 @@
                 <executions>
                     <execution>
                         <id>example-resources</id>
-                        <phase>generate-resources</phase>
+                        <phase>${sting.generate-resources.phase}</phase>
                     </execution>
                 </executions>
             </plugin>
diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml
index 3bd9f262e..b909e6ba2 100644
--- a/public/queue-package/pom.xml
+++ b/public/queue-package/pom.xml
@@ -82,10 +82,86 @@
             <classifier>example-resources</classifier>
             <type>tar.bz2</type>
         </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>queue-framework</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.google.caliper</groupId>
+            <artifactId>caliper</artifactId>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>unit-tests</id>
+                        <configuration>
+                            <skip>${sting.serialunittests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-failsafe-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>integration-tests</id>
+                        <configuration>
+                            <skip>${sting.serialintegrationtests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>pipeline-tests</id>
+                        <configuration>
+                            <skip>${sting.serialpipelinetests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>large-scale-tests</id>
+                        <configuration>
+                            <skip>${sting.seriallargescaletests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-dependency-plugin</artifactId>
@@ -163,8 +239,29 @@
                     <version>${project.version}</version>
                     <optional>true</optional>
                 </dependency>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>queue-private</artifactId>
+                    <version>${project.version}</version>
+                    <type>test-jar</type>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
             </dependencies>
         </profile>
+        <profile>
+            <id>packagetests-enabled</id>
+            <activation>
+                <property>
+                    <name>sting.packagetests.enabled</name>
+                    <value>true</value>
+                </property>
+            </activation>
+            <properties>
+                <sting.unpack.phase>none</sting.unpack.phase>
+                <sting.shade.phase>none</sting.shade.phase>
+            </properties>
+        </profile>
     </profiles>
 
 </project>
diff --git a/public/repo/net/sf/picard/1.107.1676/picard-1.107.1676.pom b/public/repo/net/sf/picard/1.107.1676/picard-1.107.1676.pom
index 6fa774352..5cb3de5fd 100644
--- a/public/repo/net/sf/picard/1.107.1676/picard-1.107.1676.pom
+++ b/public/repo/net/sf/picard/1.107.1676/picard-1.107.1676.pom
@@ -37,8 +37,8 @@
             <groupId>com.sun</groupId>
             <artifactId>tools.jar</artifactId>
             <version>1.5</version>
-            <classifier>system</classifier>
-            <systemPath>${java.home}../lib/tools.jar</systemPath>
+            <scope>system</scope>
+            <systemPath>${java.home}/../lib/tools.jar</systemPath>
         </dependency>
     </dependencies>
 </project>
diff --git a/public/sting-utils/pom.xml b/public/sting-utils/pom.xml
index 043be645f..f30d02736 100644
--- a/public/sting-utils/pom.xml
+++ b/public/sting-utils/pom.xml
@@ -17,7 +17,6 @@
         <sting.basedir>${project.basedir}/../..</sting.basedir>
         <gsalib.packagedir>org/broadinstitute/sting/utils/R</gsalib.packagedir>
         <gsalib.filename>gsalib.tar.gz</gsalib.filename>
-        <sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
     </properties>
 
     <dependencies>