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view tool_dependencies.xml @ 1:3e3356b13281

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Mon, 27 May 2013 16:52:37 +0200
parents 00e31088ff16
children 616ee8e4abf4
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<tool_dependency>
    <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>

                <!-- apply one small patched file, to support the query-format target-format commandline options -->
                <action type="download_file">http://chem-fingerprints.googlecode.com/hg-history/1281bfcb470b84f5e75250dfa041345d280dde30/chemfp/commandline/simsearch.py</action>
                <action type="shell_command">rm $INSTALL_DIR/lib/python/chemfp/commandline/simsearch.py</action>
                <action type="move_file">
                    <source>simsearch.py</source>
                    <destination>$INSTALL_DIR/lib/python/chemfp/commandline/</destination>
                </action>
                <!-- end patching -->

                <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 and rdkit as underlying toolkit.
        Compiling chemfp requires gcc and a python2.5+ version.</readme>
    </package>
</tool_dependency>