# HG changeset patch
# User mzeidler
# Date 1380045275 14400
# Node ID 226228ac32a2394f27965bf888ec8a4e4cfa81b3
# Parent  4f6e349dfc17b1ce94571f794508a5cde3f41630
Uploaded

diff -r 4f6e349dfc17 -r 226228ac32a2 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 24 13:29:20 2013 -0400
+++ b/tool_dependencies.xml	Tue Sep 24 13:54:35 2013 -0400
@@ -22,62 +22,12 @@
             </actions>
         </install>
     </package>
-        <package name="freetype" version="2.4.11">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/freetype/freetype2/2.4.11/freetype-2.4.11.tar.bz2</action>
-                <action type="shell_command">./configure --prefix=$INSTALL_DIR/freetype/</action>
-                <action type="shell_command">make</action>
-                <action type="shell_command">make install</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="append_to">$INSTALL_DIR/freetype/bin/</environment_variable>
-                    <environment_variable name="FREETYPE_LIB_DIR" action="set_to">$INSTALL_DIR/freetype/lib/</environment_variable>
-                    <environment_variable name="FREETYPE_INCLUDE_DIR" action="set_to">$INSTALL_DIR/freetype/include/</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling freetype requires a C compiler (typically gcc).</readme>
-    </package>
-
-<package name="matplotlib" version="1.3.0">
-        <install version="1.0">
-            <actions>
-                <!-- first action is always downloading -->
-                <action type="download_by_url">http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.3.0/matplotlib-1.3.0.tar.gz</action>
-
-                             
-                <!-- install matplotlib -->
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                <action type="shell_command">echo "### PYTHONPATH = $PYTHONPATH, PYTHONPATH_NUMPY = $PYTHONPATH_NUMPY"</action>
-                <action type="shell_command">export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY:$PYTHONPATH &amp;&amp;
-                                             export CPLUS_INCLUDE_PATH=$FREETYPE_INCLUDE_DIR:$FREETYPE_INCLUDE_DIR/freetype2/:$CPLUS_INCLUDE_PATH &amp;&amp; 
-                                             export LIBRARY_PATH=$FREETYPE_LIB_DIR:$LIBRARY_PATH &amp;&amp;  
-                                             python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
-                <action type="set_environment">
-                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
-                    <environment_variable action="set_to" name="PYTHONPATH_MATPLOTLIB">$INSTALL_DIR/lib/python</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling matplotlib requires a C compiler (typically gcc) and libpng.</readme>
-    </package>
 <package name="biopython" version="1.61">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action>
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
-                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
-                    export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
-                    export PYTHONPATH=$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="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
+                    python setup.py install --user
                 </action>
             </actions>
         </install>