# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1413232359 18000
# Node ID 30a8343fb0e7ca2937255becf9ee687fc1eae12c
# Parent  59459de657404279aa611b2edf5e7ec67c594a6c
Change for extra_files_path

diff -r 59459de65740 -r 30a8343fb0e7 rsem_calculate_expression.xml
--- a/rsem_calculate_expression.xml	Mon Mar 10 07:19:56 2014 -0500
+++ b/rsem_calculate_expression.xml	Mon Oct 13 15:32:39 2014 -0500
@@ -94,7 +94,7 @@
     #end if
     ## RSEM reference
     #if $reference.refSrc == 'history':
-      ${reference.rsem_ref.extra_files_path}/${reference.rsem_ref.metadata.reference_name}
+      ${reference.rsem_ref.dataset.extra_files_path}/${reference.rsem_ref.metadata.reference_name}
     #elif $reference.refSrc == 'cached':
       ${reference.index.fields.path}
     #end if
diff -r 59459de65740 -r 30a8343fb0e7 rsem_prepare_reference.xml
--- a/rsem_prepare_reference.xml	Mon Mar 10 07:19:56 2014 -0500
+++ b/rsem_prepare_reference.xml	Mon Oct 13 15:32:39 2014 -0500
@@ -6,8 +6,8 @@
   </requirements>
   <command>
     echo $reference_name " " | tee $reference_file &amp;&amp;
-    mkdir $reference_file.extra_files_path &amp;&amp; 
-    cd $reference_file.extra_files_path &amp;&amp; 
+    mkdir $reference_file.dataset.extra_files_path &amp;&amp; 
+    cd $reference_file.dataset.extra_files_path &amp;&amp; 
     rsem-prepare-reference 
     #if $polya.polya_use == 'add':
       #if $polya.polya_length: