--- a/tool_dependencies.xml	Fri Mar 23 22:26:23 2018 -0400
+++ b/tool_dependencies.xml	Fri Jun 01 17:55:23 2018 -0400
@@ -9,21 +9,12 @@
   <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="2.14">
+  <package name="dunovo" version="2.15">
     <install version="1.0">
       <actions>
         <!-- download the main dunovo package files -->
-        <action sha256sum="e517a12794e7cac31b4ebcad99e6a6c0789027ace7d33f89d06ff2bc961515fc" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.14.tar.gz</action>
+        <action sha256sum="1cf02bcc37cc641a20bdf5e20c2b3b98d4dccd43b1182830cb1a9e7d173d1a78" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.15.tar.gz</action>
         <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. -->
-        <!-- Move precheck.py and its dependencies into the main source directory. -->
-        <action type="move_file">
-          <source>utils/precheck.py</source>
-          <destination>$TMP_WORK_DIR/dunovo-2.14</destination>
-        </action>
-        <action type="move_file">
-          <source>utils/getreads.py</source>
-          <destination>$TMP_WORK_DIR/dunovo-2.14</destination>
-        </action>
         <!-- install submodules -->
         <action type="shell_command">rmdir kalign utillib ET</action>
         <!-- download the utillib submodule -->
@@ -32,15 +23,15 @@
         <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>$TMP_WORK_DIR/dunovo-2.14</destination>
+          <destination>$TMP_WORK_DIR/dunovo-2.15</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="download_file">https://github.com/makovalab-psu/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>$TMP_WORK_DIR/dunovo-2.14</destination>
+          <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
         </action>
         <!-- download the ET submodule -->
         <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
@@ -48,7 +39,28 @@
         <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>$TMP_WORK_DIR/dunovo-2.14</destination>
+          <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
+        </action>
+        <!-- download the bfx submodule -->
+        <action type="download_file">https://github.com/NickSto/bfx/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="bfx" type="move_file">
+          <source>bfx-0.2.0</source>
+          <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
+        </action>
+        <!-- Move some source files from subdirectories into the main source directory. -->
+        <action type="move_file">
+          <source>utils/precheck.py</source>
+          <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
+        </action>
+        <action type="move_file">
+          <source>bfx/trimmer.py</source>
+          <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
+        </action>
+        <action type="move_file">
+          <source>utils/getreads.py</source>
+          <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
         </action>
         <!-- make and install -->
         <action type="shell_command">make clean</action>