# HG changeset patch
# User bgruening
# Date 1378847635 14400
# Node ID 77487c05ffc7ce4c2343cc1e2e9155352ebbe49f
# Parent  c5847db0cb414f8f0b0de8123d5875fe46e7dc92
Uploaded

diff -r c5847db0cb41 -r 77487c05ffc7 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Aug 14 07:18:18 2013 -0400
+++ b/tool_dependencies.xml	Tue Sep 10 17:13:55 2013 -0400
@@ -4,15 +4,17 @@
         <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="793c48909d53" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a476c1177222" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="710c8d9bb449" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-
+    <package name="pysam" version="0.7.5">
+        <repository changeset_revision="a4e35f23093f" name="package_pysam_0_7_5" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="ucsc_tools" version="0.1">
         <install version="1.0">
             <actions>
@@ -45,11 +47,17 @@
     <package name="deepTools" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">
         <install version="1.0">
             <actions>
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">&gt;
+                    <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>
+                </action>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
                 <action type="shell_command">git reset --hard df852fa1ef13251a17274ee18fbf919fbc515079</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
-                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python: &amp;&amp; 
                     python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                 </action>