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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="lapack" version="3.4.2">
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4 <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="atlas" version="3.10.1">
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7 <repository changeset_revision="68df9078bf69" name="package_atlas_3_10" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="numpy" version="1.7.1">
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10 <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="scipy" version="0.12.0">
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13 <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="matplotlib" version="1.2.1">
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16 <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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17 </package>
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18
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19 <package name="scikit_learn" version="0.14.1">
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20 <install version="1.0">
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21 <actions>
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22 <action type="download_by_url">https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.14.1.tar.gz</action>
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23 <action type="set_environment_for_install">
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24 <repository changeset_revision="68df9078bf69" name="package_atlas_3_10" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
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25 <package name="atlas" version="3.10.1" />
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26 </repository>
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27 <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
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28 <package name="lapack" version="3.4.2" />
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29 </repository>
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30 <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
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31 <package name="numpy" version="1.7.1" />
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32 </repository>
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33 <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
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34 <package name="scipy" version="0.12.0" />
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35 </repository>
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36 <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
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37 <package name="matplotlib" version="1.2.1" />
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38 </repository>
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39 </action>
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40
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41 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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42 <action language="cheetah" type="template_command">
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43 export PYTHONPATH=\$PYTHONPATH:$env.INSTALL_DIR/lib/python &&
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44
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45 #if env.get('ATLAS_LIB_DIR', False):
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46 export ATLAS=$env.ATLAS_LIB_DIR/libatlas.a &&
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47 #end if
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48 #if env.get('LAPACK_LIB_DIR', False):
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49 export BLAS=$env.LAPACK_LIB_DIR/libblas.a &&
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50 export LAPACK=$env.LAPACK_LIB_DIR/liblapack.a &&
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51 #end if
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52
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53 export PATH=\$PATH:$env.PATH_NUMPY &&
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54 export PYTHONPATH=\$PYTHONPATH:$env.PYTHONPATH_NUMPY:$env.PYTHONPATH_SCIPY:$env.PYTHONPATH_MATPLOTLIB &&
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55
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56 python setup.py install --install-lib $env.INSTALL_DIR/lib/python
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57 </action>
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58 <action type="set_environment">
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59 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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60 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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61 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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62 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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63 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
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64 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
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65 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
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66
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67 <environment_variable action="set_to" name="PYTHONPATH_SCIKIT_LEARN">$INSTALL_DIR/lib/python</environment_variable>
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68 </action>
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69 </actions>
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70 </install>
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71 <readme>
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72 Compiling scikit-learn requires a C compiler (typically gcc).
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73 The PYTHONPATH for scikit-learn can be accessed through PYTHONPATH_SCIKIT_LEARN.
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74
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75 Wrapper development: https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies
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76 </readme>
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77 </package>
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78 </tool_dependency>
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