--- a/tool_dependencies.xml	Mon Jun 15 08:32:55 2015 -0400
+++ b/tool_dependencies.xml	Tue Jul 26 09:54:21 2016 -0400
@@ -2,10 +2,10 @@
 <tool_dependency>
   <!-- Dependencies from main/test toolsheds -->
   <package name="numpy" version="1.9">
-    <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
   <package name="R" version="3.1.2">
-    <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
   <!-- Subset of UCSC tools -->
   <package name="ucsc_tools_for_macs21" version="1.0">
@@ -45,20 +45,12 @@
               <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action>
 	      <!-- Install environment for main & test toolsheds -->
               <action type="set_environment_for_install">
-		<repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+		<repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
 		  <package name="numpy" version="1.9" />
 		</repository>
-		<repository changeset_revision="4778b172b895" name="package_atlas_3_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-		  <package name="atlas" version="3.10.2" />
-		</repository>
 	      </action>
               <action type="make_directory">$INSTALL_DIR/lib/python</action>
               <action type="shell_command">
-		echo PWD is: ;
-		pwd ;
-		echo PYTHONPATH is $PYTHONPATH ;
-		python -c "import numpy" ;
-		echo About to do the operations: ;
                 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
               </action>