<?xml version="1.0"?>
<tool_dependency>
<!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help
  partly based on : https://toolshed.g2.bx.psu.edu/repos/iuc/package_r_3_0_3
   -->
  	<package name="R_bioc_metams" version="3.1.1">
      <install version="1.0">
          <actions_group>
                <actions>
                    <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.1.tar.gz</action>
                    <action type="move_directory_files">
	                  	<source_directory>.</source_directory>
	                    <destination_directory>$INSTALL_DIR</destination_directory>
	                </action>
                    <action type="shell_command">
                        cd $INSTALL_DIR; $INSTALL_DIR/configure --libdir=$INSTALL_DIR/lib --prefix=$INSTALL_DIR
                    </action>
                    <action type="shell_command">make -C $INSTALL_DIR</action>
                </actions>
                <action type="set_environment">
                    <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/doc</environment_variable>
                    <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
                    <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/share</environment_variable>
                    <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/library</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
                <!-- the Bioconductor and metaMS part -->
                <action type="shell_command">wget -P $INSTALL_DIR http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics_r_dependencies/raw-file/tip/INSTALL.r</action>
                <action type="shell_command">$INSTALL_DIR/bin/Rscript $INSTALL_DIR/INSTALL.r</action>
            </actions_group>
        </install>
        <readme>
				Ensures R 3.1.1 is installed. 
				Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed. 
                R is a free software environment for statistical computing and graphics.
        </readme>
    </package>


</tool_dependency>