annotate tool_dependencies.xml @ 6:4229f8f239b3 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_scikit_learn_0_13 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty

<?xml version="1.0"?>
<tool_dependency>
        <package name="numpy" version="1.7.1">
            <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="scipy" version="0.12.0">
            <repository changeset_revision="cfbbe183f8a7" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
        </package>
        <package name="matplotlib" version="1.2.1">
            <repository changeset_revision="f4e53dfdd044" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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="5686c79a72d5" name="package_lapack_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="lapack" version="3.4.2" />
                        </repository>
                        <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="numpy" version="1.7.1" />
                        </repository>
                        <repository changeset_revision="cfbbe183f8a7" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="scipy" version="0.12.0" />
                        </repository>
                        <repository changeset_revision="f4e53dfdd044" name="package_matplotlib_1_2" owner="iuc" toolshed="https://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;

                    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 $env.INSTALL_DIR/lib/python
                    </action>
                    <action type="set_environment">
                        <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                        <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                        <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                        <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
                        <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
                        <environment_variable action="prepend_to" name="PYTHONPATH">$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>