# HG changeset patch
# User lparsons
# Date 1383667653 18000
# Node ID 1a69449ae02599ae719077b916f877fa32d15c2a
# Parent  7cc1db015f03ce12e7d276e1f9f75cfe536b921d
Setup numpy environment to install htseq

diff -r 7cc1db015f03 -r 1a69449ae025 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 04 16:50:35 2013 -0500
+++ b/tool_dependencies.xml	Tue Nov 05 11:07:33 2013 -0500
@@ -2,7 +2,7 @@
 <tool_dependency>
 
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="samtools" version="0.1.19">
@@ -17,6 +17,12 @@
         <install version="1.0">
             <actions>
                 <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="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.7.1" />
+                   </repository>
+                </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>