changeset 0:0852fc3ba0ec draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testing.xml	Wed Sep 23 07:32:06 2015 -0400
@@ -0,0 +1,15 @@
+<tool id="kunv02rt90uis" name="R-3-2-0" version="1.0.0">
+  <description>R version and installation test</description>
+<requirements>
+     <requirement type="set_environment">R_ROOT_DIR</requirement>
+    <requirement type="package" version="3.2.0">R</requirement>
+</requirements>
+  <command> /bin/which R > $output_file;
+            /bin/which \$R_ROOT_DIR/bin/R >> $output_file;
+            echo \$R_ROOT_DIR >> $output_file;
+            echo \$PATH >> $output_file;
+   </command>
+  <outputs>
+    <data type="data" format="txt" name="output_file" label ="output_r_3_2_0.env" />
+  </outputs>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 23 07:32:06 2015 -0400
@@ -0,0 +1,52 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.2.0">
+        <install version="1.0">
+        <actions_group>
+            <actions>
+                <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz</action>
+                 <action type="move_directory_files">
+                        <source_directory>R-3.2.0</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                <action type="shell_command">./configure --with-tcltk \
+                                    --with-blas \
+                                    --with-lapack \
+                                    --with-readline \
+                                    --with-cairo \
+                                    --with-libpng \
+                                    --without-x \
+                                    --enable-R-shlib \
+                                    --disable-R-framework \
+                                    --libdir=$INSTALL_DIR/lib \
+                                    --prefix=$INSTALL_DIR </action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
+               
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/R-3.2.0/bin</environment_variable>
+                </action>
+            </actions>
+  </actions_group>
+  </install>
+        <readme>
+        hdsj
+        </readme>
+    </package>
+    <package name="limma" version="3.24.12">
+        <install version="1.0">
+            <actions>
+				<action type="setup_r_environment">
+				<package name="R" version="3.2.0" />
+			<package>https://bioarchive.galaxyproject.org/limma_3.25.3.tar.gz</package>
+                </action>
+             </actions>
+             
+        </install>
+        <readme>
+limma_3.24.12 installed now try edgeR 
+        </readme>
+    </package>
+    
+</tool_dependency>