# HG changeset patch
# User qfab
# Date 1401410140 14400
# Node ID fbe9f90728fcde09fb5d15accf2dc25f3796bb22

Uploaded

diff -r 000000000000 -r fbe9f90728fc tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu May 29 20:35:40 2014 -0400
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<tool_dependency>
+        <package name="numpy" version="1.8.1">
+            <repository changeset_revision="36659940cecb" name="package_numpy_1_8" owner="qfab" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
+        </package>
+        <package name="pycogent" version="1.5.2">
+            <install version="1.0">
+                <actions>
+                    <action type="download_by_url">http://sourceforge.net/projects/pycogent/files/PyCogent/1.5.2/PyCogent-1.5.2.tgz/download</action>
+                    <action type="make_directory">$INSTALL_DIR/cogent</action>
+                    <action type="set_environment_for_install">
+                       <repository changeset_revision="36659940cecb" name="package_numpy_1_8" owner="qfab" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" >
+                          <package name="numpy" version="1.8.1" />
+                        </repository>
+                    <action type="shell_command">
+                      python -c "import numpy; print numpy.version.version" &amp;&amp; env >> /opt/galaxy/log.txt:
+                    </action>
+                    </action>
+                    <action type="shell_command">
+                        python setup.py build_ext -if
+                    </action>
+                    <action type="move_directory_files">
+                        <source_directory>cogent</source_directory>
+                        <destination_directory>$INSTALL_DIR/cogent/</destination_directory>
+                    </action> 
+                    <action type="set_environment">
+                       <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+                       <environment_variable action="set_to" name="PATH_PYCOGENT">$INSTALL_DIR</environment_variable>
+                       <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
+                       <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> 
+                    </action>
+                </actions>
+            </install>
+            <readme>It is required to install a numpy python package (here numpy python package version 1.8.1) before installing the pycogent package.</readme>
+        </package>
+</tool_dependency>