diff --git a/tools/encode/gencode_partition.xml b/tools/encode/gencode_partition.xml
index 415ae8a7b6c..ca22ca4333b 100755
--- a/tools/encode/gencode_partition.xml
+++ b/tools/encode/gencode_partition.xml
@@ -1,6 +1,6 @@
 <tool id="gencode_partition1" name="Gencode Partition">
   <description>an interval file</description>
-  <command interpreter="python">split_by_partitions.py /home/universe/encode_feature_partitions/partition_list.txt $input1 $out_file1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command>
+  <command interpreter="python">split_by_partitions.py ${GALAXY_DATA_INDEX_DIR} $input1 $out_file1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command>
   <inputs>
     <param name="input1" type="data" format="interval" label="File to Partition"/>
   </inputs>
diff --git a/tools/encode/split_by_partitions.py b/tools/encode/split_by_partitions.py
index 7bfd6650665..3ed95999562 100755
--- a/tools/encode/split_by_partitions.py
+++ b/tools/encode/split_by_partitions.py
@@ -18,8 +18,9 @@ def stop_err( msg ):
     sys.exit()
 
 def main():
-    partition_index = sys.argv[1]
-    partition_offset = "/home/universe/encode_feature_partitions/" #should parse perhaps from index filepath
+    GALAXY_DATA_INDEX_DIR = sys.argv[1]
+    partition_index = '%s/encode_feature_partitions/partition_list.txt' % GALAXY_DATA_INDEX_DIR
+    partition_offset = "%s/encode_feature_partitions/" % GALAXY_DATA_INDEX_DIR
     
     warnings = []