annotate tool_dependencies.xml @ 1:ededc5ef3fc0 draft

updated to point to the IUC account for external dependencies

<?xml version="1.0"?>
<tool_dependency>
    <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="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>
    <!-- TODO reportlab -> Python Imaging Library
    <package name="reportlab" version="1.2.1">
        <repository name="package_reportlab_1_2" owner="bgruening" prior_installation_required="True" />
    </package>
    -->
    <package name="biopython" version="1.61">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action>
                <action type="set_environment_for_install">
                    <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>
                    <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>
                </action>

                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                    export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY:$PYTHONPATH_MATPLOTLIB &amp;&amp; 
                    python setup.py install --install-lib $INSTALL_DIR/lib/python
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>

                    <environment_variable action="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_MATPLOTLIB]</environment_variable>

                    <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
                    </action>
            </actions>
        </install>
        <readme>The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.</readme>
    </package>
</tool_dependency>