# HG changeset patch
# User s-kaufmann
# Date 1408112389 14400
# Node ID 9a495fd2fe0f35c6b1d8620dfe38041ac236b354
# Parent  acb6cae8bfecd75d2ec4073f7588b7a359a82c95
Uploaded

diff -r acb6cae8bfec -r 9a495fd2fe0f tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Aug 15 09:49:46 2014 -0400
+++ b/tool_dependencies.xml	Fri Aug 15 10:19:49 2014 -0400
@@ -1,69 +1,97 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="JAR_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
-    </set_environment>
-
-    <set_environment version="1.0">
-	<environment_variable name="CIRCOS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-
-<package name="circos" version="0.64">
-        <install version="1.0">
-            <actions>          
-               <!-- Downloads the Circos software from its website and unpacks it -->
-               <action type="download_by_url">http://circos.ca/distribution/circos-0.64.tgz </action>
-               <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR/</destination_directory>
-               </action>                
-               <action type="set_environment">
-                        <environment_variable name="CIRCOS_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>                            
-            </actions>
-        </install>
-        <readme>
-Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed.
-        </readme>
-    </package>  
-
-    <set_environment version="1.0">
-	<environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-
     <package name="R_3_0_2" version="3.0.2">
         <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.2.tar.gz</action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
-                        <package name="readline" version="6.2" />
-                    </repository>
-                    <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
-                        <package name="ncurses" version="5.9" />
-                    </repository>
-                    <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
-                        <package name="libpng" version="1.6.7" />
-                    </repository>
-                </action>
-
-<action type="shell_command">
-                    ./configure CPPFLAGS="-I$READLINE_INCLUDE_PATH -I${LIBPNG_ROOT}/include" LDFLAGS="-L$READLINE_LIB_PATH -L$NCURSES_LIB_PATH -L${LIBPNG_ROOT}/lib -lreadline -lncurses" --with-libpng --enable-R-shlib  --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR --datarootdir=$INSTALL_DIR/share/
+            <actions_group>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.2-Darwin-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.2-Linux-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                    <action type="set_environment">
+                        <environment_variable action="set_to" name="TCL_LIBRARY">$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>
+                </actions>
+                <actions>
+                    <package name="readline" version="6.2">
+                        <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="libpng" version="1.6.7">
+                        <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="cairo" version="1.12.14">
+                        <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="pixman" version="0.32.4">
+                        <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="freetype" version="2.5.2">
+                        <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    </package>
+                    <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.2.tar.gz</action>
+                    <action type="set_environment_for_install">
+                        <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="readline" version="6.2" />
+                        </repository>
+                        <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="libpng" version="1.6.7" />
+                        </repository>
+                        <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="cairo" version="1.12.14" />
+                        </repository>
+                        <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="pixman" version="0.32.4" />
+                        </repository>
+                        <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <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=$INSTALL_DIR 
+                    </action>
+                    <action type="make_install" />
+                    <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
+                    <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="R_ROOT_DIR">$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>
-
-                <action type="shell_command">make</action>
-                <action type="shell_command">make install</action>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
-                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
-                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
-                    <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
-                </action>
-            </actions>
+            </actions_group>
         </install>
-        <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
+        <readme>
+        The precompiled versions were built 2014-03-07.       
+        R is a free software environment for statistical computing and graphics. http://www.r-project.org/
+        </readme>
     </package>
-
 </tool_dependency>