--- a/tool_dependencies.xml	Mon Nov 03 10:30:29 2014 -0500
+++ b/tool_dependencies.xml	Sun Mar 29 12:54:10 2015 -0400
@@ -1,22 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="bowtie" version="0.12.7">
-      <repository changeset_revision="f54826948b0b" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
       <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="pysam" version="0.7.7">
-      <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="R" version="3.0.3">
-      <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biocbasics" version="2.14">
       <install version="1.0">
           <actions>
               <action type="set_environment_for_install">
-                  <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                  <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                       <package name="R" version="3.0.3" />
                     </repository>
                 </action>
@@ -31,6 +31,12 @@
                 <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
             </actions>
         </install>
+    <package name="numpy" version="1.9">
+        <repository name="package_numpy_1_9" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="scipy" version="0.14">
+        <repository name="package_scipy_0_14" owner="iuc" prior_installation_required="True" />
+    </package>
         <readme>Installs some basic bioc packages for the lattice wrapper and grid + gridExtra for managing lattice panels
         It's clunky but this is the most convenient way iuc could get anything installed into the package_r3
         Note we use cran at fred hutch since no fastest mirror thingy