diff --git a/java/build.xml b/java/build.xml
index 826208bbd..b1fb3f21b 100644
--- a/java/build.xml
+++ b/java/build.xml
@@ -1,4 +1,4 @@
-<project name="AnalysisTK" default="dist" basedir=".">
+<project name="AnalysisTK" default="dist" basedir="." xmlns:ivy="antlib:org.apache.ivy.ant">
     <description>
         simple build file
     </description>
@@ -7,7 +7,27 @@
   <property name="build" location="build"/>
   <property name="dist"  location="dist"/>
   <property name="lib"  location="lib"/>
-  
+
+  <!-- ivy properties -->
+  <property name="ivy.install.version" value="2.0.0" />
+  <property name="ivy.home" value="${user.home}/.ant" />
+  <property name="ivy.jar.dir" value="${ivy.home}/lib" />
+  <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar" />
+  <property name="ivy.settings.dir" value="settings" />
+  <property file="${ivy.settings.dir}/ivysettings.properties" />
+
+  <target name="resolve">
+    <mkdir dir="${ivy.jar.dir}" />
+    <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
+         dest="${ivy.jar.dir}/${ivy.jar.file}" 
+         usetimestamp="true"/>
+    <taskdef resource="org/apache/ivy/ant/antlib.xml" 
+             uri="antlib:org.apache.ivy.ant" 
+             classpath="${ivy.jar.dir}/${ivy.jar.file}" />
+    <ivy:settings file="${ivy.settings.dir}/ivysettings.xml" />
+    <ivy:retrieve />
+  </target>
+
   <target name="init">
     <!-- Create the time stamp -->
     <tstamp/>
@@ -15,7 +35,7 @@
     <mkdir dir="${build}"/>
   </target>
 
-  <target name="compile" depends="init"
+  <target name="compile" depends="init,resolve"
         description="compile the source " >
     <!-- Compile the java code from ${src} into ${build} -->
     <javac srcdir="${src}" destdir="${build}" >
@@ -35,7 +55,7 @@
     <!-- Put everything in ${build} into the MyProject-${DSTAMP}.jar file -->
     <jar jarfile="${dist}/AnalysisTK.jar" basedir="${build}">
       <manifest>
-        <attribute name="Class-Path" value="functionalj.jar picard.jar sam-1.0.jar" />
+        <attribute name="Class-Path" value="functionalj-1.0.jar picard-snapshot.jar sam-1.0.jar" />
         <attribute name="Main-Class" value="edu.mit.broad.sting.atk.AnalysisTK" />
       </manifest>
     </jar>
@@ -50,5 +70,6 @@
     <!-- Delete the ${build} and ${dist} directory trees -->
     <delete dir="${build}"/>
     <delete dir="${dist}"/>
+    <delete dir="${lib}" />
   </target>
 </project>
diff --git a/java/ivy.xml b/java/ivy.xml
new file mode 100644
index 000000000..a76fa3ca7
--- /dev/null
+++ b/java/ivy.xml
@@ -0,0 +1,8 @@
+<ivy-module version="1.0">
+  <info organisation="edu.mit.broad" module="Sting"/>
+  <dependencies>
+    <dependency org="net.sf" name="functionalj" rev="latest.integration" />
+    <dependency org="net.sf" name="sam" rev="latest.integration" />
+    <dependency name="picard" rev="latest.integration" />
+  </dependencies>
+</ivy-module>
diff --git a/java/settings/ivysettings.properties b/java/settings/ivysettings.properties
new file mode 100644
index 000000000..8a67434f9
--- /dev/null
+++ b/java/settings/ivysettings.properties
@@ -0,0 +1 @@
+repository.dir=${ivy.settings.dir}/repository
diff --git a/java/settings/ivysettings.xml b/java/settings/ivysettings.xml
new file mode 100644
index 000000000..5cacb105a
--- /dev/null
+++ b/java/settings/ivysettings.xml
@@ -0,0 +1,16 @@
+<ivysettings>
+  <properties file="${ivy.settings.dir}/ivysettings.properties"/>
+  <settings defaultResolver="libraries"/>
+  <resolvers>
+    <filesystem name="projects">
+	 <artifact pattern="${repository.dir}/[organisation]/[artifact]-[revision].[ext]" />
+	 <ivy pattern="${repository.dir}/[organisation]/[module]-[revision].xml" />
+    </filesystem>
+    <ibiblio name="libraries" m2compatible="true" usepoms="false" />
+  </resolvers>
+  <modules>
+    <module organisation="edu.mit.broad" resolver="projects" />
+    <module organisation="net.sf" module="functionalj" resolver="projects" />
+    <module organisation="net.sf" module="samtools" resolver="projects" />
+  </modules>
+</ivysettings>
diff --git a/java/lib/picard.jar b/java/settings/repository/edu.mit.broad/picard-snapshot.jar
similarity index 100%
rename from java/lib/picard.jar
rename to java/settings/repository/edu.mit.broad/picard-snapshot.jar
diff --git a/java/settings/repository/edu.mit.broad/picard-snapshot.xml b/java/settings/repository/edu.mit.broad/picard-snapshot.xml
new file mode 100644
index 000000000..0fbb75283
--- /dev/null
+++ b/java/settings/repository/edu.mit.broad/picard-snapshot.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="edu.mit.broad" module="picard" revision="snapshot" status="integration" />
+</ivy-module>
diff --git a/java/lib/functionalj.jar b/java/settings/repository/net.sf/functionalj-1.0.jar
similarity index 100%
rename from java/lib/functionalj.jar
rename to java/settings/repository/net.sf/functionalj-1.0.jar
diff --git a/java/settings/repository/net.sf/functionalj-1.0.xml b/java/settings/repository/net.sf/functionalj-1.0.xml
new file mode 100644
index 000000000..2d57ef884
--- /dev/null
+++ b/java/settings/repository/net.sf/functionalj-1.0.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="functionalj" revision="1.0" status="release" />
+</ivy-module>
diff --git a/java/lib/sam-1.0.jar b/java/settings/repository/net.sf/sam-1.0.jar
similarity index 100%
rename from java/lib/sam-1.0.jar
rename to java/settings/repository/net.sf/sam-1.0.jar
diff --git a/java/settings/repository/net.sf/sam-1.0.xml b/java/settings/repository/net.sf/sam-1.0.xml
new file mode 100644
index 000000000..8ecabcb10
--- /dev/null
+++ b/java/settings/repository/net.sf/sam-1.0.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.0" status="release" />
+</ivy-module>