Merge pull request #531 from broadinstitute/ks_build_patches

Build patches

pom.xml

@@ -715,6 +715,14 @@
                         <id>unlink-public-testdata</id>
                         <phase>clean</phase>
                     </execution>
+                    <execution>
+                        <id>link-public-qscript</id>
+                        <phase>process-test-resources</phase>
+                    </execution>
+                    <execution>
+                        <id>unlink-public-qscript</id>
+                        <phase>clean</phase>
+                    </execution>
                 </executions>
             </plugin>
             <plugin>
@@ -802,6 +810,33 @@
             <modules>
                 <module>private</module>
             </modules>
+            <build>
+                <plugins>
+                    <!-- TODO: All tests require access to private. For now. -->
+                    <plugin>
+                        <groupId>com.pyx4j</groupId>
+                        <artifactId>maven-junction-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>link-private-testdata</id>
+                                <phase>process-test-resources</phase>
+                            </execution>
+                            <execution>
+                                <id>unlink-private-testdata</id>
+                                <phase>clean</phase>
+                            </execution>
+                            <execution>
+                                <id>link-private-qscript</id>
+                                <phase>process-test-resources</phase>
+                            </execution>
+                            <execution>
+                                <id>unlink-private-qscript</id>
+                                <phase>clean</phase>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
         </profile>
 
         <!-- Collection of properties for use during package testing -->

protected/gatk-protected/pom.xml

@@ -31,8 +31,8 @@
         </dependency>
 
         <dependency>
-            <groupId>gov.nist</groupId>
+            <groupId>gov.nist.math</groupId>
-            <artifactId>Jama</artifactId>
+            <artifactId>jama</artifactId>
         </dependency>
 
         <dependency>

public/external-example/pom.xml

@@ -26,6 +26,9 @@
         <sting.committests.skipped>true</sting.committests.skipped>
         <sting.unittests.skipped>${sting.committests.skipped}</sting.unittests.skipped>
         <sting.integrationtests.skipped>${sting.committests.skipped}</sting.integrationtests.skipped>
+
+        <!-- This flag is used by the package tests to disable re-shading -->
+        <sting.shade.phase>package</sting.shade.phase>
     </properties>
 
     <repositories>
@@ -128,7 +131,7 @@
                 <version>2.1</version>
                 <executions>
                     <execution>
-                        <phase>package</phase>
+                        <phase>${sting.shade.phase}</phase>
                         <goals>
                             <goal>shade</goal>
                         </goals>
@@ -246,4 +249,19 @@
         </plugins>
     </build>
 
+    <profiles>
+        <profile>
+            <id>packagetests-enabled</id>
+            <activation>
+                <property>
+                    <name>sting.packagetests.enabled</name>
+                    <value>true</value>
+                </property>
+            </activation>
+            <properties>
+                <sting.shade.phase>none</sting.shade.phase>
+            </properties>
+        </profile>
+    </profiles>
+
 </project>

public/gatk-package/pom.xml

@@ -57,6 +57,7 @@
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
             <type>test-jar</type>
+            <scope>test</scope>
         </dependency>
 
         <dependency>

public/queue-framework/pom.xml

@@ -61,6 +61,14 @@
             <scope>runtime</scope>
         </dependency>
 
+        <!--
+        NOTE: Because exec-maven-plugin is used, this aggregator dependency
+        will cause mvn compile to not work. Use mvn test-compile for now.
+
+        See:
+          http://stackoverflow.com/questions/4786881/why-is-test-jar-dependency-required-for-mvn-compile
+          http://jira.codehaus.org/browse/MEXEC-91
+        -->
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
@@ -78,6 +86,9 @@
 
     <build>
         <plugins>
+            <!--
+            See note above about exec plugin breaking mvn compile
+            -->
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>

public/queue-package/pom.xml

@@ -88,6 +88,7 @@
             <artifactId>queue-framework</artifactId>
             <version>${project.version}</version>
             <type>test-jar</type>
+            <scope>test</scope>
         </dependency>
 
         <dependency>
@@ -95,6 +96,7 @@
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
             <type>test-jar</type>
+            <scope>test</scope>
         </dependency>
 
         <dependency>

public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom

@@ -1,9 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>com.google.code.caliper</groupId>
-  <artifactId>caliper</artifactId>
-  <name>caliper</name>
-  <version>1.0-SNAPSHOT</version>
-</project>

public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom

@@ -1,9 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>gov.nist</groupId>
-  <artifactId>Jama</artifactId>
-  <name>Jama</name>
-  <version>1.0.2</version>
-</project>

public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.pom

@@ -1,9 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>net.sf.gridscheduler</groupId>
-  <artifactId>drmaa</artifactId>
-  <name>drmaa</name>
-  <version>6.2u5p2</version>
-</project>

public/sting-root/pom.xml

@@ -141,8 +141,8 @@
                 <version>1.6.1</version>
             </dependency>
             <dependency>
-                <groupId>gov.nist</groupId>
+                <groupId>gov.nist.math</groupId>
-                <artifactId>Jama</artifactId>
+                <artifactId>jama</artifactId>
                 <version>1.0.2</version>
             </dependency>
             <dependency>
@@ -201,9 +201,9 @@
                 <version>0.8.1</version>
             </dependency>
             <dependency>
-                <groupId>net.sf.gridscheduler</groupId>
+                <groupId>us.levk</groupId>
-                <artifactId>drmaa</artifactId>
+                <artifactId>drmaa-gridengine</artifactId>
-                <version>6.2u5p2</version>
+                <version>6.2u5</version>
             </dependency>
             <dependency>
                 <groupId>net.sf.snpeff</groupId>
@@ -531,6 +531,7 @@
                     </extraArguments>
                     <setReactorProjectsProperties>true</setReactorProjectsProperties>
                     <descriptionProperty>git.version</descriptionProperty>
+                    <failOutput>exported</failOutput>
                 </configuration>
                 <executions>
                     <execution>

public/sting-utils/pom.xml

@@ -93,8 +93,8 @@
             <artifactId>jets3t</artifactId>
         </dependency>
         <dependency>
-            <groupId>net.sf.gridscheduler</groupId>
+            <groupId>us.levk</groupId>
-            <artifactId>drmaa</artifactId>
+            <artifactId>drmaa-gridengine</artifactId>
         </dependency>
         <dependency>
             <groupId>com.google.code.gson</groupId>