annotate tool_dependencies.xml @ 2:b482933a6de5 draft

biopython version only with hard dependencies

<?xml version="1.0"?>
<tool_dependency>
    <package name="numpy" version="1.7.1">
        <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </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="74c21f9bdc39" 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>