annotate tool_dependencies.xml @ 0:31c9c5014965 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_1_1 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.1.1">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="darwin">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.1.1-Darwin-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                    <action type="shell_command">sh $INSTALL_DIR/darwin_post_install.sh $INSTALL_DIR</action>
                </actions>
                <actions architecture="x86_64" os="linux">
                   <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.1.1.tar.gz</action>
                   <package name="readline" version="6.2">
                        <repository name="package_readline_6_2" owner="iuc" prior_installation_required="True" />
                    </package>
                    <package name="libpng" version="1.6.7">
                        <repository  name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" />
                    </package>
                    <package name="cairo" version="1.12.14">
                        <repository name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" />
                    </package>
                    <package name="pixman" version="0.32.4">
                        <repository name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" />
                    </package>
                    <package name="freetype" version="2.5.2">
                        <repository name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" />
                    </package>
                    <action type="set_environment">
                        <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
                        <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
                    </action>
                    <action type="set_environment_for_install">
                        <repository name="package_readline_6_2" owner="iuc" prior_installation_required="True" >
                            <package name="readline" version="6.2" />
                        </repository>
                        <repository name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" >
                            <package name="libpng" version="1.6.7" />
                        </repository>
                        <repository name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" >
                            <package name="cairo" version="1.12.14" />
                        </repository>
                        <repository name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" >
                            <package name="pixman" version="0.32.4" />
                        </repository>
                        <repository name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" >
                            <package name="freetype" version="2.5.2" />
                        </repository>
                    </action>
                    <action type="shell_command">
                        export LDFLAGS="-L$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$READLINE_INCLUDE_PATH" &amp;&amp;
                        ./configure --with-tcltk \
                                    --with-blas \
                                    --with-lapack \
                                    --with-readline \
                                    --with-cairo \
                                    --with-libpng \
                                    --without-x \
                                    --enable-R-shlib \
                                    --disable-R-framework \
                                    --libdir=$INSTALL_DIR/lib \
                                    --prefix=$INSTALL_DIR 
                    </action>
                    <action type="make_install" />
                    <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
                    <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
                </actions>
                <action type="set_environment">
                    <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
                    <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
                    <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
                    <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
                    <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
                    <environment_variable action="set_to" name="RHOME">$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/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
                Using Rstudio cran which seems to be properly versioned.
                darwin needs work - I have no mac access...
                R is a free software environment for statistical computing and graphics.
                NOTE: See custom compilation options above.
        </readme>
    </package>
</tool_dependency>