--- a/tool_dependencies.xml	Fri Nov 10 09:33:29 2017 -0500
+++ b/tool_dependencies.xml	Fri Jan 12 19:18:41 2018 -0500
@@ -1,21 +1,47 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="bowtie2" version="2.2.5">
-    <repository changeset_revision="30bd7eaeddbf" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="samtools" version="0.1.18">
-    <repository changeset_revision="1409782220c9" name="package_samtools_0_1_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="bowtie" version="1.1.2">
+    <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="mafft" version="7.221">
-    <repository changeset_revision="15974dd17515" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="c5908940967d" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="networkx" version="1.10">
     <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="dunovo" version="2.0.9">
+  <package name="dunovo" version="2.0.12">
     <install version="1.0">
       <actions>
-        <action sha256sum="6f5295b8eae0e161ee3bd28829ca140657743c695624ffc7f467f13eab2c547c" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.9.tar.gz</action>
+        <!-- download the main dunovo package files -->
+        <action sha256sum="6973f163dabf82d236982534d88b5d11573a5aa0982bf9d6236be635fb9b4e11" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.12.tar.gz</action>
+        <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. -->
+        <action type="shell_command">rmdir kalign utillib ET</action>
+        <!-- download the utillib submodule -->
+        <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
+        <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
+        <action type="shell_command">rm v0.1.0.tar.gz</action>
+        <action rename_to="utillib" type="move_file">
+          <source>utillib-0.1.0</source>
+          <destination>$TMP_WORK_DIR/dunovo-2.0.12</destination>
+        </action>
+        <!-- download the kalign submodule -->
+        <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action>
+        <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
+        <action type="shell_command">rm v0.2.0.tar.gz</action>
+        <action rename_to="kalign" type="move_file">
+          <source>kalign-dunovo-0.2.0</source>
+          <destination>$TMP_WORK_DIR/dunovo-2.0.12</destination>
+        </action>
+        <!-- download the ET submodule -->
+        <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
+        <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action>
+        <action type="shell_command">rm v0.2.2.tar.gz</action>
+        <action rename_to="ET" type="move_file">
+          <source>ET-0.2.2</source>
+          <destination>$TMP_WORK_DIR/dunovo-2.0.12</destination>
+        </action>
+        <!-- make and install -->
+        <action type="shell_command">make clean</action>
         <action type="shell_command">make</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
@@ -24,8 +50,6 @@
         <action type="set_environment">
           <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
         </action>
-        <!-- Note: This does not install the submodules.
-        Functionality they provide will not be available. -->
       </actions>
     </install>
   </package>