--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Nov 03 10:29:28 2014 -0500
@@ -0,0 +1,38 @@
+<?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" />
+    </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" />
+    </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" />
+    </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">
+                      <package name="R" version="3.0.3" />
+                    </repository>
+                </action>
+                <action type="make_directory">$INSTALL_DIR</action>
+                <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" &gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "source(bioclite)" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "installme=c(\"lattice\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
+            </actions>
+        </install>
+        <readme>Installs some basic bioc packages for the lattice wrapper 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
+       </readme>
+    </package>
+</tool_dependency>