view tool_dependencies.xml @ 1:0f560efd398f draft

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<?xml version="1.0"?>
<tool_dependency>
        <package name="lapack" version="3.4.2">
            <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
        </package>
        <package name="atlas" version="3.10.1">
            <repository changeset_revision="68df9078bf69" name="package_atlas_3_10" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
        </package>
        <package name="numpy" version="1.7.1">
            <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
        </package>
        <package name="scipy" version="0.12.0">
            <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
        </package>
        <package name="matplotlib" version="1.2.1">
            <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.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="68df9078bf69" name="package_atlas_3_10" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="atlas" version="3.10.1" />
                        </repository>
                        <repository changeset_revision="a6b8f46acca7" name="package_lapack_3_4" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="lapack" version="3.4.2" />
                        </repository>
                        <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="numpy" version="1.7.1" />
                        </repository>
                        <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                            <package name="scipy" version="0.12.0" />
                        </repository>
                        <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" toolshed="http://testtoolshed.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>