diff tool_dependencies.xml @ 3:ae9dda584395 draft

Removed trace of MatPlotLib

--- a/tool_dependencies.xml	Mon Aug 12 11:29:41 2013 -0400
+++ b/tool_dependencies.xml	Tue Sep 17 04:54:28 2013 -0400
@@ -4,6 +4,17 @@
         <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="biopython" version="1.61">
+        <readme>
+This Galaxy Tool Shed package installs Biopython from source, having
+first installed NumPy which is a build time depencency. This requires
+and assumes a standard C compiler is already installed, along with
+the Python header files.
+
+Development of this dependency definition is being done here on GitHub:
+https://github.com/biopython/galaxy_packages
+
+The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
+        </readme>
         <install version="1.0">
             <actions>
                 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action>
@@ -16,20 +27,16 @@
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                     export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
-                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY:$PYTHONPATH_MATPLOTLIB &amp;&amp; 
+                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp; 
                     python setup.py install --install-lib $INSTALL_DIR/lib/python
                 </action>
                 <action type="set_environment">
                     <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-
                     <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                     <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
-                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
-
                     <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
-                    </action>
+                </action>
             </actions>
         </install>
-        <readme>The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.</readme>
     </package>
 </tool_dependency>