From 2e99a6ecf848a1ba75eb42c39243b591d5e31afd Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Sat, 15 Feb 2014 01:12:32 +0800
Subject: [PATCH] Create symlinks target/GenomeAnalysisTK.jar and
 target/Queue.jar during package phase.

---
 pom.xml                      | 15 +++++++++++++++
 public/gatk-package/pom.xml  |  4 ++++
 public/queue-package/pom.xml |  4 ++++
 3 files changed, 23 insertions(+)

diff --git a/pom.xml b/pom.xml
index 6b3703c89..d45f4a413 100644
--- a/pom.xml
+++ b/pom.xml
@@ -511,6 +511,21 @@
                                 </links>
                             </configuration>
                         </execution>
+                        <execution>
+                            <id>link-binary-jar</id>
+                            <goals>
+                                <goal>link</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <links>
+                                    <link>
+                                        <dst>${sting.basedir}/target/${sting.binary-dist.name}.${project.packaging}</dst>
+                                        <src>${project.build.directory}/${project.build.finalName}.${project.packaging}</src>
+                                    </link>
+                                </links>
+                            </configuration>
+                        </execution>
                         <execution>
                             <id>link-git-release</id>
                             <goals>
diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml
index 1e9bb5bc9..881058949 100644
--- a/public/gatk-package/pom.xml
+++ b/public/gatk-package/pom.xml
@@ -170,6 +170,10 @@
                 <groupId>com.pyx4j</groupId>
                 <artifactId>maven-junction-plugin</artifactId>
                 <executions>
+                    <execution>
+                        <id>link-binary-jar</id>
+                        <phase>${sting.shade.phase}</phase>
+                    </execution>
                     <execution>
                         <id>link-git-release</id>
                         <phase>${sting.shade.phase}</phase>
diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml
index 790eeac72..eda2fd98f 100644
--- a/public/queue-package/pom.xml
+++ b/public/queue-package/pom.xml
@@ -208,6 +208,10 @@
                 <groupId>com.pyx4j</groupId>
                 <artifactId>maven-junction-plugin</artifactId>
                 <executions>
+                    <execution>
+                        <id>link-binary-jar</id>
+                        <phase>${sting.shade.phase}</phase>
+                    </execution>
                     <execution>
                         <id>link-git-release</id>
                         <phase>${sting.shade.phase}</phase>