--- a/tool_dependencies.xml	Mon Mar 11 12:44:45 2013 -0400
+++ b/tool_dependencies.xml	Tue Nov 05 13:02:43 2013 -0500
@@ -1,31 +1,34 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="numpy" version="1.6.2">
+
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="picard" version="1.56.0">
+        <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="htseq" version="0.5.4p5">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</action>
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
-                <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action>
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.7.1" />
+                   </repository>
                 </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-
-    <package name="htseq" version="0.5.4p1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
                 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
                 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                 <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>
         </install>
@@ -34,44 +37,4 @@
         </readme>
     </package>
 
-    <package name="samtools" version="0.1.18">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
-                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>misc/maq2sam-long</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Compiling SAMtools requires the ncurses and zlib development libraries.
-        </readme>
-    </package>
-
-    <package name="picard" version="1.56.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
-                <action type="move_directory_files">
-                    <source_directory>picard-tools-1.56</source_directory>
-                    <destination_directory>$INSTALL_DIR/jars</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
 </tool_dependency>