diff --git a/build.xml b/build.xml
index 6a0281a16..c98b49056 100644
--- a/build.xml
+++ b/build.xml
@@ -178,6 +178,24 @@
           </manifest>
         </jar>
 
+        <jar jarfile="${dist.dir}/MarkAllAlignmentsAsPrimary.jar" whenmanifestonly="skip">
+          <fileset dir="build">
+            <include name="**/*.class" />
+          </fileset>
+          <manifest>
+            <attribute name="Main-Class" value="org.broadinstitute.sting.oneoffprojects.tools.MarkAllAlignmentsAsPrimary" />
+          </manifest>
+        </jar>
+
+        <jar jarfile="${dist.dir}/RepairSeattleBAM.jar" whenmanifestonly="skip">
+          <fileset dir="build">
+            <include name="**/*.class" />
+          </fileset>
+          <manifest>
+            <attribute name="Main-Class" value="org.broadinstitute.sting.oneoffprojects.tools.RepairSeattleBAM" />
+          </manifest>
+        </jar>
+
 	   <jar jarfile="${dist.dir}/VCFTool.jar" whenmanifestonly="skip">
           <fileset dir="build">
             <include name="**/*.class"/>
@@ -222,6 +240,18 @@
                 <attribute name="Class-Path" value="${jar.classpath}" />
             </manifest>
         </jar>
+
+        <jar jarfile="${dist.dir}/MarkAllAlignmentsAsPrimary.jar" update="true" whenmanifestonly="skip">
+            <manifest>
+                <attribute name="Class-Path" value="${jar.classpath}" />
+            </manifest>
+        </jar>
+
+        <jar jarfile="${dist.dir}/RepairSeattleBAM.jar" update="true" whenmanifestonly="skip">
+            <manifest>
+                <attribute name="Class-Path" value="${jar.classpath}" />
+            </manifest>
+        </jar>
     </target>
 
     <target name="core" description="force a build of the Sting core code">