<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="2.11.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://cran.rstudio.com/src/base/R-2/R-2.11.0.tar.gz</action>
                <action type="shell_command">
                    ./configure --enable-R-shlib \
                    --with-readline=no \
                    --with-x=no \
                    --prefix=$INSTALL_DIR \
                    --libdir=$INSTALL_DIR/lib \
                    --disable-R-framework
                </action>
                <action type="shell_command">make &amp;&amp; make install</action>
                <action type="set_environment">
                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            R is a free software environment for statistical computing and graphics.
            NOTE: See custom compilation options above 
        </readme>
    </package>
    <package name="numpy" version="1.7.1">
        <repository toolshed="http://toolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="iuc" changeset_revision="74c21f9bdc39" />
    </package>
    <package name="rseqc" version="2.3.7">
        <install version = "1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
                <action type="shell_command">python setup.py install --root $INSTALL_DIR --prefix . --install-lib lib</action>
                <action type="set_environment">
                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/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#.
            Requires gcc, python, numpy, and R
        </readme>
    </package>

</tool_dependency>