view tool_dependencies.xml @ 8:d241ff83e485

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<tool_dependency>
    <package name="rdkit" version="2012_12_1">
        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_rdkit_2012_12" owner="bgruening" changeset_revision="0adc830e7d71" />
    </package>
    <package name="numpy" version="1.7.1">
        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="c3041382815c" />
    </package>
    <package name="matplotlib" version="1.2.1">
        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_matplotlib_1_2" owner="bgruening" changeset_revision="ae165d9e610a" />
    </package>

    <package name="chemfp" version="1.1p1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://chem-fingerprints.googlecode.com/files/chemfp-1.1p1.tar.gz</action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        The core chemfp functionality does not depend on a third-party library but you will need a chemistry toolkit in order to generate new fingerprints 
        from structure files. chemfp supports the free Open Babel and RDKit toolkits and the proprietary OEChem toolkit.
        Currently the Galaxy-wrappers are using openbabel as underlying toolkit.
        Compiling chemfp requires gcc and a python2.5+ version.</readme>
    </package>
</tool_dependency>