annotate tool_dependencies.xml @ 1:ed025c662e59 draft default tip

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<?xml version='1.0' encoding='utf-8'?>
<tool_dependency>
    <package name="python" version="2.7.10">
        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="pyvcf" version="0.6.7">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/P/PyVCF/PyVCF-0.6.7.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="python" version="2.7.10" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="make_directory">$INSTALL_DIR/lib/python/bin</action>
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/lib/python/bin
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="append_to" name="PATH">$INSTALL_DIR/lib/python/bin</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_PYVCF">$INSTALL_DIR/lib/python</environment_variable>
                </action>
            </actions>
        </install>
            <readme>
            This Galaxy Tool shed package installs pyvcf(https://pypi.python.org/pypi/PyVCF)
            package for use with python 2.7.10.

            The corresponding PYTHONPATH is accessible via PYTHONPATH_PYVCF
        </readme>
    </package>
</tool_dependency>