# HG changeset patch
# User iuc
# Date 1432062075 14400
# Node ID 31c9c501496521d1987d3c334c7e0e92a4ed67d4

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

diff -r 000000000000 -r 31c9c5014965 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 19 15:01:15 2015 -0400
@@ -0,0 +1,97 @@
+<?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>