--- a/tool_dependencies.xml	Thu Nov 14 05:43:15 2013 -0500
+++ b/tool_dependencies.xml	Thu Nov 28 12:58:28 2013 -0500
@@ -12,8 +12,8 @@
     <package name="scipy" version="0.12.0">
         <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="pysam" version="0.7.6">
-        <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="pysam" version="0.7.7">
+        <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="ucsc_tools" version="0.1">
@@ -54,17 +54,17 @@
          <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
      </package>
 
-    <package name="deepTools" version="1.5.1_91b873c095bb4ca44da99e57d8b49784508aa98b">
+    <package name="deepTools" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">
         <install version="1.0">
             <actions>
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="a4e35f23093f" name="package_pysam_0_7_5" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="pysam" version="0.7.5" />
+                    <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="pysam" version="0.7.7" />
                     </repository>
                 </action>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
-                <action type="shell_command">git reset --hard 91b873c095bb4ca44da99e57d8b49784508aa98b</action>
+                <action type="shell_command">git reset --hard 323fa6bf083c9d40e5092a6364a4ab8fee57507a</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
@@ -73,7 +73,7 @@
 
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                     <!-- disable the config file of deepTools -->
                     <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
                 </action>