Merge pull request #727 from broadinstitute/ks_gatk_queue_package_test_updates

Various fixes for package tests.

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -359,6 +359,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
 
     @Test
     public void testInvalidJexl() {
+        // NOTE: JexlEngine singleton construction in VariantContextUtils sets silent to false.
+        // However VariantFiltration.initialize() sets setSilent(true) on the shared instance.
+        // Just in case this test runs after a VariantFiltration in the same VM, always set silent back to false.
+        htsjdk.variant.variantcontext.VariantContextUtils.engine.get().setSilent(false);
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants" +
                         " -R "+b37KGReference +

public/external-example/pom.xml

@@ -28,6 +28,7 @@
         <gatk.integrationtests.skipped>${gatk.committests.skipped}</gatk.integrationtests.skipped>
 
         <!-- This flag is used by the package tests to disable re-shading -->
+        <gatk.unpack.phase>process-resources</gatk.unpack.phase>
         <gatk.shade.phase>package</gatk.shade.phase>
     </properties>
 
@@ -73,7 +74,7 @@
                 <executions>
                     <execution>
                         <id>unpack</id>
-                        <phase>process-resources</phase>
+                        <phase>${gatk.unpack.phase}</phase>
                         <goals>
                             <goal>unpack</goal>
                         </goals>
@@ -261,6 +262,8 @@
                 </property>
             </activation>
             <properties>
+                <gatk.jar.phase>none</gatk.jar.phase>
+                <gatk.unpack.phase>none</gatk.unpack.phase>
                 <gatk.shade.phase>none</gatk.shade.phase>
             </properties>
         </profile>

public/package-tests/pom.xml

@@ -102,6 +102,7 @@
                             <!-- TODO: Using additionalClasspathElement while debugging exclusion issue above -->
                             <additionalClasspathElements>
                                 <additionalClasspathElement>${gatk.basedir}/public/gatk-tools-public/target/gatk-tools-public-${project.version}-tests.jar</additionalClasspathElement>
+                                <additionalClasspathElement>${gatk.basedir}/public/gatk-queue/target/gatk-queue-${project.version}-tests.jar</additionalClasspathElement>
                             </additionalClasspathElements>
                         </configuration>
                         <executions>
@@ -142,7 +143,8 @@
                             <testClassesDirectory>${gatk.packagetests.testClasses}</testClassesDirectory>
                             <!-- TODO: Using additionalClasspathElement while debugging exclusion issue above -->
                             <additionalClasspathElements>
-                                <additionalClasspathElement>${gatk.basedir}/public/gatk-framework/target/gatk-framework-${project.version}-tests.jar</additionalClasspathElement>
+                                <additionalClasspathElement>${gatk.basedir}/public/gatk-tools-public/target/gatk-tools-public-${project.version}-tests.jar</additionalClasspathElement>
+                                <additionalClasspathElement>${gatk.basedir}/public/gatk-queue/target/gatk-queue-${project.version}-tests.jar</additionalClasspathElement>
                             </additionalClasspathElements>
                         </configuration>
                         <executions>