# HG changeset patch
# User Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
# Date 1441193000 -3600
# Node ID 99dda3e399975c23758fc6f31c980f659064384d
# Parent  4b125431980240596a8a7841ecedbb988638dc1a
Attempt 4 using virtualenv

diff -r 4b1254319802 -r 99dda3e39997 ribocount.xml
--- a/ribocount.xml	Tue Sep 01 17:50:38 2015 +0100
+++ b/ribocount.xml	Wed Sep 02 12:23:20 2015 +0100
@@ -7,7 +7,7 @@
     <stdio>
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
-    <command interpreter="python">${RIBOPLOT_PATH}/ribocount
+    <command>python \${RIBOPLOT_PATH}/ribocount
     --ribo_file "${ribo_file}"
     --transcriptome_fasta "${transcriptome_fasta}"
     --read_length "${read_length}"
diff -r 4b1254319802 -r 99dda3e39997 riboplot.xml
--- a/riboplot.xml	Tue Sep 01 17:50:38 2015 +0100
+++ b/riboplot.xml	Wed Sep 02 12:23:20 2015 +0100
@@ -7,7 +7,7 @@
     <stdio>
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
-    <command interpreter="python">${RIBOPLOT_PATH}/riboplot
+    <command>python \${RIBOPLOT_PATH}/riboplot
     --ribo_file "${ribo_file}"
     --transcriptome_fasta "${transcriptome_fasta}"
     --transcript_name "${transcript_name}"
diff -r 4b1254319802 -r 99dda3e39997 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 01 17:50:38 2015 +0100
+++ b/tool_dependencies.xml	Wed Sep 02 12:23:20 2015 +0100
@@ -5,9 +5,7 @@
             <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">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="RIBOPLOT_PATH">$INSTALL_DIR/venv/bin</environment_variable>
                 </action>
             </actions>
         </install>