view rgedgeR/tool_dependencies.xml @ 3:e22b0320a4ff draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="readline" version="6.2">
        <repository changeset_revision="1301ec7705a8" name="package_readline_6_2" owner="boris" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    <package name="package_R" version="3.0.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="1301ec7705a8" name="package_readline_6_2" owner="boris" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                        <package name="readline" version="6.2" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR</action>
                <action type="shell_command">./configure --with-blas --with-lapack --enable-R-shlib --with-readline=no --with-x=no --prefix=$INSTALL_DIR &amp;&amp; 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
                WARNING: See custom compilation options above
                Modified from an older version of R by Boris by Ross Lazarus for R 3.0
                Added Bioc basics too
       </readme>
    </package>
    <package name="package_BioCBasics" version="2.12">
        <install version="1.0">
            <actions>
                <action type="shell_command">$INSTALL_DIR/lib/R/bin/R CMD BATCH installBioC.R </action>
            </actions>
        </install>
        <readme>R is a free software environment for statistical computing and graphics
                WARNING: See custom compilation options above
                Modified from an older version of R by Boris by Ross Lazarus for R 3.0
                Added Bioc basics via this package installBioC.R script
       </readme>
    </package>
</tool_dependency>