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view tool_dependencies.xml @ 1:f92b87abef3d

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author nilesh
date Thu, 18 Jul 2013 10:54:06 -0500
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<?xml version="1.0"?>
<tool_dependency>
    
    <package name="rseqc" version="2.3.7">
        <install version = "1.0">
            <actions>
                <action type="download_by_url">https://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/rnaseqc/RNA-SeQC_v1.1.7.jar</action>
                <action type="shell_command">python setup.py install --root $INSTALL_DIR/lib/rseqc</action>
                <action type="set_environment">
                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/rseqc/usr/local/lib/python2.7/site-packages</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/lib/rseqc/usr/local/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        	RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#.
        </readme>
    </package>
    
</tool_dependency>