diff --git a/build.xml b/build.xml
index a2f85c448..c808a8a0e 100644
--- a/build.xml
+++ b/build.xml
@@ -110,30 +110,6 @@
           </manifest>
         </jar>
     
-        <jar jarfile="dist/SomaticCoverage.jar" whenmanifestonly="skip">
-          <fileset dir="build">
-            <include name="**/somaticcoverage/*.class"/>
-            <include name="**/walkers/SomaticCoverageWalker.class"/>
-            
-          </fileset>
-          <fileset dir="java">
-            <include name="**/somaticcoverage/*.xml"/>
-          </fileset>
-            <manifest>
-            <attribute name="Main-Class" value="org.broadinstitute.sting.playground.somaticcoverage.SomaticCoverageTool" />
-          </manifest>
-        </jar>
-
-
-        <jar jarfile="dist/AnnotateSecondaryBase.jar" whenmanifestonly="skip">
-          <fileset dir="build">
-            <include name="**/secondarybase/**/*.class" />
-          </fileset>
-          <manifest>
-            <attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.AnnotateSecondaryBase" />
-          </manifest>
-        </jar>
-
         <jar jarfile="dist/Playground.jar" whenmanifestonly="skip">
             <fileset dir="build">
                 <include name="**/*.class"/>
@@ -165,23 +141,11 @@
             </manifest>
         </jar>
 
-        <jar jarfile="dist/AnnotateSecondaryBase.jar" update="true" whenmanifestonly="skip">
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}" />
-            </manifest>
-        </jar>
-
         <jar jarfile="dist/Playground.jar" update="true" whenmanifestonly="skip">
             <manifest>
                 <attribute name="Class-Path" value="${jar.classpath}"/>
             </manifest>
         </jar>
-        
-        <jar jarfile="dist/SomaticCoverage.jar" update="true" whenmanifestonly="skip">
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}"/>
-            </manifest>
-        </jar>
     </target>
 
     <target name="core" description="force a build of the Sting core code">
diff --git a/java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java b/java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java
index a77a81353..c4251ca44 100644
--- a/java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java
+++ b/java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java
@@ -70,11 +70,7 @@ public class SomaticCoverageTool extends CommandLineExecutable {
 
     /** override any arguments we see fit. */
     protected void overrideArguments() {
-        try {
-            this.argCollection = GATKArgumentCollection.unmarshal(this.getClass().getResource("/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverage.xml").openStream());
-        } catch (IOException e) {
-            throw new RuntimeException(e);
-        }
+        this.argCollection = GATKArgumentCollection.unmarshal(getClass().getClassLoader().getResourceAsStream("SomaticCoverage.xml"));
         this.argCollection.samFiles = samFiles;
     }
 }
diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl
index b4b1873b3..5a9b5825e 100644
--- a/packages/CreatePackager.xsl
+++ b/packages/CreatePackager.xsl
@@ -26,6 +26,9 @@
             <root classname="{current()}" />
           </xsl:for-each>
         </classfileset>
+        <xsl:for-each select="dependencies/file">
+          <fileset file="{current()}" />
+        </xsl:for-each>
         <manifest>
           <attribute name="Main-Class" value="{main-class}"/>
         </manifest>
diff --git a/packages/SomaticCoverage.xml b/packages/SomaticCoverage.xml
new file mode 100644
index 000000000..f0520c611
--- /dev/null
+++ b/packages/SomaticCoverage.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>SomaticCoverage</name>
+  <main-class>org.broadinstitute.sting.playground.somaticcoverage.SomaticCoverageTool</main-class>
+  <dependencies>
+    <class>org.broadinstitute.sting.playground.gatk.walkers.SomaticCoverageWalker</class>
+    <file>java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverage.xml</file>
+  </dependencies>
+</package>