# HG changeset patch
# User iuc
# Date 1376218450 14400
# Node ID ef6c2c1cf49e724ef4483714416b8a684fd352a9

initial upload

diff -r 000000000000 -r ef6c2c1cf49e tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sun Aug 11 06:54:10 2013 -0400
@@ -0,0 +1,78 @@
+<?xml version="1.0"?>
+<tool_dependency>
+        <package name="lapack" version="3.4.2">
+            <repository changeset_revision="98a7d116c15f" name="package_lapack_3_4" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="atlas" version="3.10.1">
+            <repository changeset_revision="597c0e54eded" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="numpy" version="1.7.1">
+            <repository changeset_revision="c75482be1d3a" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="scipy" version="0.12.0">
+            <repository changeset_revision="aa5180c893f5" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="matplotlib" version="1.2.1">
+            <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        </package>
+
+        <package name="scikit_learn" version="0.14.1">
+            <install version="1.0">
+                <actions>
+                    <action type="download_by_url">https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.14.1.tar.gz</action>
+                    <action type="set_environment_for_install">
+                        <repository changeset_revision="597c0e54eded" name="package_atlas_3_10" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                            <package name="atlas" version="3.10.1" />
+                        </repository>
+                        <repository changeset_revision="98a7d116c15f" name="package_lapack_3_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                            <package name="lapack" version="3.4.2" />
+                        </repository>
+                        <repository changeset_revision="c75482be1d3a" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                            <package name="numpy" version="1.7.1" />
+                        </repository>
+                        <repository changeset_revision="aa5180c893f5" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                            <package name="scipy" version="0.12.0" />
+                        </repository>
+                        <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                            <package name="matplotlib" version="1.2.1" />
+                        </repository>
+                    </action>
+
+                    <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                    <action language="cheetah" type="template_command">
+                    export PYTHONPATH=\$PYTHONPATH:$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;
+
+                    python setup.py install --install-lib $env.INSTALL_DIR/lib/python
+                    </action>
+                    <action type="set_environment">
+                        <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                        <environment_variable action="append_to" name="PYTHONPATH">$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_SCIPY]</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
+                        <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
+
+                        <environment_variable action="set_to" name="PYTHONPATH_SCIKIT_LEARN">$INSTALL_DIR/lib/python</environment_variable>
+                        </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.
+            
+            Wrapper development: https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies
+            </readme>
+        </package>
+</tool_dependency>