diff --git a/lib/galaxy/datatypes/test/test.gff b/lib/galaxy/datatypes/test/test.gff
index 4630d0ff78e..450ecbcd88f 100644
--- a/lib/galaxy/datatypes/test/test.gff
+++ b/lib/galaxy/datatypes/test/test.gff
@@ -1,7 +1,7 @@
 # gff-version 2
 ## Date: Thu Dec 8 19:46:27 2005
 ## bed2gff.pl $Rev: 601 $
-## Input file: /cache/ftp/encode/datasets/msa.AR.20051208.bed
+## Input file: /depot/data2/galaxy/encode-data/datasets/msa.AR.20051208.bed
 
 chr7	bed2gff	AR	26731313	26731437	.	+	.	score "0";
 chr7	bed2gff	AR	26731491	26731536	.	+	.	score "0";
diff --git a/tools/data_source/encode_import.py b/tools/data_source/encode_import.py
index 5e9d2096fd9..e70e94ddd9a 100755
--- a/tools/data_source/encode_import.py
+++ b/tools/data_source/encode_import.py
@@ -24,7 +24,7 @@ while have_none:
 #create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files
 available_files = {}
 try:
-    for line in open( "/cache/encode_datasets/encode_datasets.loc" ):
+    for line in open( "/depot/data2/galaxy/encode_datasets.loc" ):
         if line[0:1] == "#" : continue
         
         fields = line.split('\t')
diff --git a/tools/data_source/encode_import_code.py b/tools/data_source/encode_import_code.py
index cce1331bdef..5ea566191ea 100644
--- a/tools/data_source/encode_import_code.py
+++ b/tools/data_source/encode_import_code.py
@@ -3,7 +3,7 @@ import os, sys
 encode_sets= {}
 
 try:
-    for line in open( "/cache/encode_datasets/encode_datasets.loc" ):
+    for line in open( "/depot/data2/galaxy/encode_datasets.loc" ):
         if line[0:1] == "#" : continue
         
         fields = line.split('\t')
diff --git a/tools/encode/random_intervals.py b/tools/encode/random_intervals.py
index 325c2cc9f96..63dfa66dec0 100644
--- a/tools/encode/random_intervals.py
+++ b/tools/encode/random_intervals.py
@@ -126,7 +126,7 @@ def main():
     
     available_regions = {}
 
-    loc_file = "/cache/regions/regions.loc"
+    loc_file = "/depot/data2/galaxy/regions.loc"
 
 
     try:
diff --git a/tools/encode/random_intervals_code.py b/tools/encode/random_intervals_code.py
index 6d0d6e48ef4..7473ac3dbcd 100644
--- a/tools/encode/random_intervals_code.py
+++ b/tools/encode/random_intervals_code.py
@@ -3,7 +3,7 @@ import os, sys
 #available_regions[build][uids]
 available_regions = {}
 
-loc_file = "/cache/regions/regions.loc"
+loc_file = "/depot/data2/galaxy/regions.loc"
 
 
 try:
diff --git a/tools/encode/random_intervals_no_bits.py b/tools/encode/random_intervals_no_bits.py
index 6307ccf7be7..0dffb1f1231 100644
--- a/tools/encode/random_intervals_no_bits.py
+++ b/tools/encode/random_intervals_no_bits.py
@@ -52,7 +52,7 @@ def main():
     
     available_regions = {}
 
-    loc_file = "/cache/regions/regions.loc"
+    loc_file = "/depot/data2/galaxy/regions.loc"
 
 
     try:
diff --git a/tools/extract/interval2maf.py b/tools/extract/interval2maf.py
index 6acb4ad34b2..1a276219316 100755
--- a/tools/extract/interval2maf.py
+++ b/tools/extract/interval2maf.py
@@ -41,7 +41,7 @@ def __main__():
     #dictionary of available maf files
     maf_sets = {}
     try:
-        for line in open( "/cache/maf/maf_index.loc" ):
+        for line in open( "/depot/data2/galaxy/maf_index.loc" ):
             if line[0:1] == "#" : continue
             fields = line.split('\t')
             #read each line, if not enough fields, go to next line
diff --git a/tools/extract/interval2maf_code.py b/tools/extract/interval2maf_code.py
index 42e098b4862..06c46d8f403 100644
--- a/tools/extract/interval2maf_code.py
+++ b/tools/extract/interval2maf_code.py
@@ -3,7 +3,7 @@ import os, sys
 maf_sets = {}
 
 try:
-    for line in open( "/cache/maf/maf_index.loc" ):
+    for line in open( "/depot/data2/galaxy/maf_index.loc" ):
         if line[0:1] == "#" : continue
         
         fields = line.split('\t')
diff --git a/tools/extract/phastOdds/phastOdds_tool.py b/tools/extract/phastOdds/phastOdds_tool.py
index 6403d09607b..049c6c72b27 100644
--- a/tools/extract/phastOdds/phastOdds_tool.py
+++ b/tools/extract/phastOdds/phastOdds_tool.py
@@ -1,5 +1,5 @@
 scores = {}
-for line in open( '/cache/phastOdds_precomputed/index.txt' ):
+for line in open( '/depot/data2/galaxy/phastOdds.loc' ):
     fields = line.strip().split( "\t" )
     if not fields[0] in scores: scores[fields[0]] = []
     scores[ fields[0] ].append( (fields[1],fields[2]) )
diff --git a/tools/stats/aggregate_binned_scores_in_intervals_code.py b/tools/stats/aggregate_binned_scores_in_intervals_code.py
index 41779e4d1a8..f9720806464 100644
--- a/tools/stats/aggregate_binned_scores_in_intervals_code.py
+++ b/tools/stats/aggregate_binned_scores_in_intervals_code.py
@@ -1,5 +1,5 @@
 scores = {}
-for line in open( '/cache/binned_scores/index.txt' ):
+for line in open( '/depot/data2/galaxy/binned_scores.loc' ):
     fields = line.strip().split( "\t" )
     if not fields[0] in scores: scores[fields[0]] = []
     scores[ fields[0] ].append( (fields[1],fields[2]) )