<?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>
                	<package name="readline" version="6.2">
                      <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="libpng" version="1.6.7">
                      <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="cairo" version="1.12.14">
                      <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="pixman" version="0.32.4">
                      <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="freetype" version="2.5.2">
                      <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
                    </package>
                    <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.1.tar.gz</action>
                    <action type="set_environment_for_install">
                      <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
                          <package name="readline" version="6.2" />
                        </repository>
                        <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
                          <package name="libpng" version="1.6.7" />
                        </repository>
                        <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
                          <package name="cairo" version="1.12.14" />
                        </repository>
                        <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
                          <package name="pixman" version="0.32.4" />
                        </repository>
                        <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
                          <package name="freetype" version="2.5.2" />
                        </repository>
                    </action>
                    <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 $INSTALL_DIR; 
                        export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" &amp;&amp;
                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &amp;&amp;
                        export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
                        export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
                        export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
                        export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
                        $INSTALL_DIR/configure  --with-tcltk \
			                                    --with-blas \
			                                    --with-lapack \
			                                    --with-readline \
			                                    --with-cairo \
			                                    --with-libpng \
			                                    --without-x \
			                                    --enable-R-shlib \
			                                    --disable-R-framework \
			                                    --libdir=$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>