# HG changeset patch
# User bgruening
# Date 1384866959 18000
# Node ID 4779579ef7e2632bd60cac25488361091a102bbc
# Parent  84b82d4df8b89b533c16025e60e95a7505ae1d7f
Uploaded

diff -r 84b82d4df8b8 -r 4779579ef7e2 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Sep 12 07:19:26 2013 -0400
+++ b/tool_dependencies.xml	Tue Nov 19 08:15:59 2013 -0500
@@ -1,36 +1,26 @@
 <?xml version="1.0"?>
 <tool_dependency>
-        <package name="lapack" version="3.4.2">
-            <repository changeset_revision="60957bd68fe2" name="package_lapack_3_4" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-        </package>
-        <package name="atlas" version="3.10.1">
-            <repository changeset_revision="3508de0ebae1" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-        </package>
         <package name="numpy" version="1.7.1">
-            <repository changeset_revision="b7ff4a8c58df" 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" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
         </package>
         <package name="scipy" version="0.12.0">
-            <repository changeset_revision="8ed7d7b6907a" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+            <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
         </package>
         <package name="matplotlib" version="1.2.1">
             <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
         </package>
-
         <package name="scikit_learn" version="0.13.1">
             <install version="1.0">
                 <actions>
                     <action type="download_by_url">https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.13.1.tar.gz</action>
                     <action type="set_environment_for_install">
-                        <repository changeset_revision="3508de0ebae1" name="package_atlas_3_10" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                            <package name="atlas" version="3.10.1" />
-                        </repository>
-                        <repository changeset_revision="60957bd68fe2" name="package_lapack_3_4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="73854db866e7" name="package_lapack_3_4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                             <package name="lapack" version="3.4.2" />
                         </repository>
-                        <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" 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 name="numpy" version="1.7.1" />
                         </repository>
-                        <repository changeset_revision="8ed7d7b6907a" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                             <package name="scipy" version="0.12.0" />
                         </repository>
                         <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
@@ -42,14 +32,6 @@
                     <action language="cheetah" type="template_command">
                     export PYTHONPATH=\$PYTHONPATH:$env.INSTALL_DIR/lib/python &amp;&amp; 
 
-                    #if env.get('ATLAS_LIB_DIR', False):
-                        export ATLAS=$env.ATLAS_LIB_DIR/libatlas.a &amp;&amp; 
-                    #end if
-                    #if env.get('LAPACK_LIB_DIR', False):
-                        export BLAS=$env.LAPACK_LIB_DIR/libblas.a &amp;&amp; 
-                        export LAPACK=$env.LAPACK_LIB_DIR/liblapack.a &amp;&amp; 
-                    #end if
-
                     export PATH=\$PATH:$env.PATH_NUMPY &amp;&amp; 
                     export PYTHONPATH=\$PYTHONPATH:$env.PYTHONPATH_NUMPY:$env.PYTHONPATH_SCIPY:$env.PYTHONPATH_MATPLOTLIB &amp;&amp;
 
@@ -68,6 +50,11 @@
                         </action>
                 </actions>
             </install>
-            <readme>Compiling scikit-learn requires a C compiler (typically gcc). The PYTHONPATH for scikit-learn can be accessed through PYTHONPATH_SCIKIT_LEARN.</readme>
+            <readme>
+            Compiling scikit-learn requires a C compiler (typically gcc). 
+            The PYTHONPATH for scikit-learn can be accessed through PYTHONPATH_SCIKIT_LEARN.
+            
+            Wrapper development: https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies
+            </readme>
         </package>
 </tool_dependency>