# HG changeset patch
# User Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
# Date 1441126238 -3600
# Node ID 4b125431980240596a8a7841ecedbb988638dc1a
# Parent  80d8e91e8b46bdfe18f47527d11e285ed9ab0e2d
Attempt 3 using virtualenv

diff -r 80d8e91e8b46 -r 4b1254319802 ribocount.xml
--- a/ribocount.xml	Tue Sep 01 17:12:59 2015 +0100
+++ b/ribocount.xml	Tue Sep 01 17:50:38 2015 +0100
@@ -7,7 +7,7 @@
     <stdio>
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
-    <command>ribocount
+    <command interpreter="python">${RIBOPLOT_PATH}/ribocount
     --ribo_file "${ribo_file}"
     --transcriptome_fasta "${transcriptome_fasta}"
     --read_length "${read_length}"
diff -r 80d8e91e8b46 -r 4b1254319802 riboplot.xml
--- a/riboplot.xml	Tue Sep 01 17:12:59 2015 +0100
+++ b/riboplot.xml	Tue Sep 01 17:50:38 2015 +0100
@@ -7,7 +7,7 @@
     <stdio>
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
-    <command>riboplot
+    <command interpreter="python">${RIBOPLOT_PATH}/riboplot
     --ribo_file "${ribo_file}"
     --transcriptome_fasta "${transcriptome_fasta}"
     --transcript_name "${transcript_name}"
diff -r 80d8e91e8b46 -r 4b1254319802 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 01 17:12:59 2015 +0100
+++ b/tool_dependencies.xml	Tue Sep 01 17:50:38 2015 +0100
@@ -4,6 +4,11 @@
         <install version="1.0">
             <actions>
                 <action type="setup_virtualenv">riboplot==0.1.0</action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="RIBOPLOT_PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
             </actions>
         </install>
         <readme>