# HG changeset patch
# User bgruening
# Date 1375443173 14400
# Node ID 4dba1ce455da578c165216f668738ed4c3c0c382
# Parent  b095bc4c481dad5636d49e9d49e630fb9fc23753
Uploaded

diff -r b095bc4c481d -r 4dba1ce455da tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jul 15 17:31:58 2013 -0400
+++ b/tool_dependencies.xml	Fri Aug 02 07:32:53 2013 -0400
@@ -3,6 +3,9 @@
     <package name="atlas" version="3.10.1">
         <repository changeset_revision="68df9078bf69" name="package_atlas_3_10" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="readline" version="6.2">
+        <repository changeset_revision="b936498ae90c" name="package_readline_6_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="R_3_0_1" version="3.0.1">
         <install version="1.0">
             <actions>
@@ -11,6 +14,9 @@
                     <repository changeset_revision="68df9078bf69" name="package_atlas_3_10" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="atlas" version="3.10.1" />
                     </repository>
+                    <repository changeset_revision="b936498ae90c" name="package_readline_6_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="readline" version="6.2" />
+                    </repository>
                 </action>
 
                 <action language="cheetah" type="template_command">
@@ -27,7 +33,7 @@
                         #set $cmd += ' --with-readline=no '
                     #end if
 
-                    #set $cmd += ' --enable-R-shlib  --with-x=no --prefix=%s ' % $env.INSTALL_DIR
+                    #set $cmd += ' --enable-R-shlib  --with-x=no --libdir=%s/lib/ --bindir=%s/bin/ --rsharedir=%s/share/' % ($env.INSTALL_DIR, $env.INSTALL_DIR, $env.INSTALL_DIR)
                     $cmd
                 </action>
                 <action type="shell_command">make</action>
@@ -37,6 +43,12 @@
                     <environment_variable action="set_to" name="R_LIBS">$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>
+
+export RHOME=$R_HOME
+export R_PATH=$R_HOME/bin
+
                 </action>
             </actions>
         </install>