# HG changeset patch
# User bgruening
# Date 1370537487 14400
# Node ID b8ccbad1b0627e3c22dd3ef91b71d9ebfb5e0829
# Parent  3c5116448979547109685d966466f65c2d8b1ac3
Uploaded

diff -r 3c5116448979 -r b8ccbad1b062 augustus.xml
--- a/augustus.xml	Thu Jun 06 12:20:31 2013 -0400
+++ b/augustus.xml	Thu Jun 06 12:51:27 2013 -0400
@@ -29,10 +29,12 @@
         #if $protein or $codingseq:
             | python extract_features.py 
                 #if $protein:
-                    --protein $protein_output 
+                    --protein $protein_output
+                #end if
                 #if $codingseq:
                     --codingseq $codingseq_output
-
+                #end if
+        #end if
     </command>
     <inputs>
         <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
diff -r 3c5116448979 -r b8ccbad1b062 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 06 12:20:31 2013 -0400
+++ b/tool_dependencies.xml	Thu Jun 06 12:51:27 2013 -0400
@@ -1,5 +1,8 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
     <package name="augustus" version="2.7">
         <install version="1.0">
             <actions>