view offtarget/tool_dependencies.xml @ 0:94332d4947cb draft default tip

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<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="2.15.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action>
                <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
                <action type="shell_command">make</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
                <action type="setup_r_environment">
                    <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.8.0.tar.gz</package>
                    <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.22.0.tar.gz</package>
                    <package>http://bioinformatics.mdanderson.org/OOMPA/2.15/src/contrib/oompaBase_3.0.1.tar.gz</package>
                    <package>http://bioinformatics.mdanderson.org/OOMPA/2.15/src/contrib/ClassComparison_3.0.0.tar.gz</package>
                    <package>http://cran.r-project.org/src/contrib/glmnet_1.9-5.tar.gz</package>
                </action>
            </actions>
        </install>
        <readme>You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.</readme>
    </package>
</tool_dependency>