From cd52cabd48c5973bac0d068b6a4eb33c06e3b7b2 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 21 Mar 2008 18:31:39 +0000
Subject: [PATCH] Eliminated hard-codes paths to locally cached data from
 tools, requires developers to add softlinks to development environments.
 Galaxy developers should execute the following commands in their
 $UNIVERSE_HOME/tool-data directories:

ln -s /depot/data2/galaxy/alignseq.loc alignseq.loc
ln -s /depot/data2/galaxy/binned_scores.loc binned_scores.loc
ln -s /depot/data2/galaxy/blastdb.loc blastdb.loc
ln -s /depot/data2/galaxy/encode_datasets.loc encode_datasets.loc
ln -s /depot/data2/galaxy/liftOver.loc liftOver.loc
ln -s /depot/data2/galaxy/maf_index.loc maf_index.loc
ln -s /depot/data2/galaxy/maf_pairwise.loc maf_pairwise.loc
ln -s /depot/data2/galaxy/microbes/microbial_data.loc microbial_data.loc
ln -s /depot/data2/galaxy/phastOdds.loc phastOdds.loc
ln -s /depot/data2/galaxy/quality_scores.loc quality_scores.loc
ln -s /depot/data2/galaxy/regions.loc regions.loc
ln -s /depot/data2/galaxy/twobit.loc twobit.loc
---
 lib/galaxy/tools/__init__.py                  |  2 +
 .../tools/parameters/dynamic_options.py       | 18 ++---
 lib/galaxy/tools/parameters/validation.py     |  3 +-
 lib/galaxy/tools/util/maf_utilities.py        |  2 +-
 setup_paths.sh                                |  7 +-
 tool-data/blastdb.loc.sample                  |  9 +++
 tool-data/liftOver.loc.sample                 | 73 +++++++++----------
 tool-data/quality_scores.loc.sample           |  6 +-
 tools/data_source/encode_import.py            |  4 +-
 .../encode_import_all_latest_datasets.xml     |  4 +-
 ...ncode_import_chromatin_and_chromosomes.xml |  4 +-
 tools/data_source/encode_import_gencode.xml   |  4 +-
 .../encode_import_genes_and_transcripts.xml   |  4 +-
 ...import_multi-species_sequence_analysis.xml |  4 +-
 ...encode_import_transcription_regulation.xml |  4 +-
 tools/data_source/microbial_import.py         |  3 +-
 tools/data_source/microbial_import.xml        | 18 ++---
 tools/data_source/microbial_import_code.py    |  4 +-
 tools/encode/random_intervals.xml             |  2 +-
 tools/encode/random_intervals_no_bits.py      |  2 +-
 tools/extract/extractAxt_wrapper.pl           |  4 +-
 tools/extract/extractAxt_wrapper.xml          |  2 +-
 tools/extract/extract_genomic_dna.py          |  4 +-
 tools/extract/extract_genomic_dna.xml         |  3 +-
 tools/extract/liftOver_wrapper.py             |  2 +-
 tools/extract/liftOver_wrapper.xml            |  2 +-
 tools/extract/phastOdds/phastOdds_tool.xml    |  2 +-
 tools/filters/axt_to_lav.xml                  |  2 +-
 tools/maf/genebed_maf_to_fasta.xml            |  4 +-
 tools/maf/interval2maf.xml                    |  2 +-
 tools/maf/interval2maf_pairwise.xml           |  4 +-
 tools/maf/interval_maf_to_merged_fasta.xml    |  4 +-
 tools/maf/maf_stats.xml                       |  2 +-
 tools/maf/maf_stats_code.py                   |  4 +-
 tools/metag_tools/blat_wrapper.py             |  8 +-
 tools/metag_tools/megablast_wrapper.py        |  2 +-
 tools/regVariation/quality_filter.xml         |  2 +-
 .../aggregate_binned_scores_in_intervals.xml  |  2 +-
 38 files changed, 127 insertions(+), 105 deletions(-)
 create mode 100644 tool-data/blastdb.loc.sample

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 4737e7cdfcd..c9275be3cd7 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -990,6 +990,8 @@ class Tool:
         # But this method of generating additional datasets should be considered DEPRECATED
         # TODO: path munging for cluster/dataset server relocatability
         param_dict['__new_file_path__'] = os.path.abspath(self.app.config.new_file_path)
+        # The following points to location (xxx.loc) files which are pointers to locally cached data
+        param_dict['GALAXY_DATA_INDEX_DIR'] = os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
         # Return the dictionary of parameters
         return param_dict
     
diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
index da1da32bbdc..78c6b67cd2e 100644
--- a/lib/galaxy/tools/parameters/dynamic_options.py
+++ b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -18,16 +18,16 @@ class DynamicOptions( object ):
         self.validators = []
 
         # Parse the options tag
-        self.from_file = elem.get( 'from_file', None )
-        if self.from_file is not None:
-            self.from_file = self.from_file.strip()
-            try: 
-                i = self.from_file.rindex( "/" )
-                self.data_file = self.from_file[ i+1: ]
-            except:
-                self.data_file = self.from_file
+        self.data_file = elem.get( 'from_file', None )
+        if self.data_file is not None:
+            self.data_file = self.data_file.strip()
+            if self.data_file.startswith( 'static' ):
+                # static files ( ucsc/builds.txt, etc ) have relative paths in the tool config
+                self.from_file = self.data_file
+            else:
+                self.from_file = "%s/%s" % ( os.environ.get( 'GALAXY_DATA_INDEX_DIR' ), self.data_file )
         else: 
-            self.data_file = None
+            self.from_file = None
         self.name_col = elem.get( 'name_col', None )
         if self.name_col is not None:
             self.name_col = int( self.name_col.strip() )
diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 17c60c345cb..0dcd054dda4 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -2,7 +2,7 @@
 Classes related to parameter validation.
 """
 
-import re, logging
+import os, re, logging
 from elementtree.ElementTree import XML
 from galaxy import model
 
@@ -222,6 +222,7 @@ class MetadataInFileColumnValidator( Validator ):
         self.metadata_name = metadata_name
         self.message = message
         self.valid_values = []
+        filename = "%s/%s" % ( os.environ.get( 'GALAXY_DATA_INDEX_DIR' ), filename )
         for line in open( filename ):
             if line_startswith is None or line.startswith( line_startswith ):
                 fields = line.split( split )
diff --git a/lib/galaxy/tools/util/maf_utilities.py b/lib/galaxy/tools/util/maf_utilities.py
index 9706ffdeab9..066091c0032 100644
--- a/lib/galaxy/tools/util/maf_utilities.py
+++ b/lib/galaxy/tools/util/maf_utilities.py
@@ -9,7 +9,7 @@ import bx.intervals
 import bx.interval_index_file
 import sys, os, string, tempfile
 
-MAF_LOCATION_FILE = "/depot/data2/galaxy/maf_index.loc"
+MAF_LOCATION_FILE = "%s/maf_index.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
 
 #an object corresponding to a reference layered alignment
 class RegionAlignment( object ):
diff --git a/setup_paths.sh b/setup_paths.sh
index 2b55bf35d8c..ff32e55d80d 100644
--- a/setup_paths.sh
+++ b/setup_paths.sh
@@ -14,7 +14,12 @@ echo "Architecture appears to be $ARCH $PYTHON_UCS"
 UNIVERSE_HOME=`pwd`
 PYTHONPATH=$UNIVERSE_HOME/lib:$UNIVERSE_HOME/eggs/$PYTHON_UCS:$UNIVERSE_HOME/eggs
 
-export UNIVERSE_HOME PYTHONPATH
+# The following directory must include location ( xxx.loc ) files that point to the
+# location where the locally cached data is stored.  These location files are used
+# by various tools.
+GALAXY_DATA_INDEX_DIR=$UNIVERSE_HOME/tool-data
+
+export UNIVERSE_HOME PYTHONPATH GALAXY_DATA_INDEX_DIR
 
 ## For PBS - if you need to force node paths (i.e. the arch the frontend
 ## runs on is not the same arch as the compute nodes or Galaxy is
diff --git a/tool-data/blastdb.loc.sample b/tool-data/blastdb.loc.sample
new file mode 100644
index 00000000000..c27c605011a
--- /dev/null
+++ b/tool-data/blastdb.loc.sample
@@ -0,0 +1,9 @@
+#This is a sample file distributed with Galaxy that is used by some
+#short read tools.  The blastdb.loc file has this format (white space 
+#characters are TAB characters):
+#
+#TODO: fill in this format
+#
+nt	/depot/data2/galaxy/blastdb/nt/nt.chunk.00 /depot/data2/galaxy/blastdb/nt/nt.chunk.01 /depot/data2/galaxy/blastdb/nt/nt.chunk.02 /depot/data2/galaxy/blastdb/nt/nt.chunk.03 /depot/data2/galaxy/blastdb/nt/nt.chunk.04 /depot/data2/galaxy/blastdb/nt/nt.chunk.05 /depot/data2/galaxy/blastdb/nt/nt.chunk.06 /depot/data2/galaxy/blastdb/nt/nt.chunk.07 /depot/data2/galaxy/blastdb/nt/nt.chunk.08 /depot/data2/galaxy/blastdb/nt/nt.chunk.09 /depot/data2/galaxy/blastdb/nt/nt.chunk.10 /depot/data2/galaxy/blastdb/nt/nt.chunk.11 /depot/data2/galaxy/blastdb/nt/nt.chunk.12 /depot/data2/galaxy/blastdb/nt/nt.chunk.13 /depot/data2/galaxy/blastdb/nt/nt.chunk.14 /depot/data2/galaxy/blastdb/nt/nt.chunk.15 /depot/data2/galaxy/blastdb/nt/nt.chunk.16 /depot/data2/galaxy/blastdb/nt/nt.chunk.17 /depot/data2/galaxy/blastdb/nt/nt.chunk.18 /depot/data2/galaxy/blastdb/nt/nt.chunk.19 /depot/data2/galaxy/blastdb/nt/nt.chunk.20 /depot/data2/galaxy/blastdb/nt/nt.chunk.21 /depot/data2/galaxy/blastdb/nt/nt.chunk.22 /depot/data2/galaxy/blastdb/nt/nt.chunk.23
+nr	/depot/data2/galaxy/blastdb/nr/nr.chunk.0 /depot/data2/galaxy/blastdb/nr/nr.chunk.1 /depot/data2/galaxy/blastdb/nr/nr.chunk.2
+test	/depot/data2/galaxy/blastdb/test/test.fa
diff --git a/tool-data/liftOver.loc.sample b/tool-data/liftOver.loc.sample
index 729fe81fb14..b956fd7a735 100644
--- a/tool-data/liftOver.loc.sample
+++ b/tool-data/liftOver.loc.sample
@@ -2,40 +2,39 @@
 #liftOver tools.  The liftOver.loc file has this format (white space 
 #characters are TAB characters):
 #
-#<FromSpecies>	<ToSpecies>
-#
-anoCar1	galGal3
-anoCar1	gasAcu1
-anoCar1	hg18
-anoCar1	mm8
-anoCar1	mm9
-anoCar1	ornAna1
-anoCar1	xenTro2
-anoGam1	dm2
-anoGam1	dm3
-apiMel1	dm2
-apiMel2	dm2
-bosTau2	bosTau3
-bosTau2	hg17
-bosTau2	hg18
-bosTau2	mm7
-bosTau2	mm8
-bosTau2	rn4
-canFam1	canFam2
-canFam1	hg17
-canFam1	mm5
-canFam1	mm6
-canFam2	equCab1
-canFam2	hg17
-canFam2	hg18
-canFam2	mm6
-canFam2	mm7
-canFam2	mm8
-canFam2	mm9
-canFam2	rn3
-canFam2	rn4
-ce2	ce4
-ce4	caePb1
-ce4	caeRem2
-ce4	cb3
-ce4	priPac1
+#<FromSpecies>	<ToSpecies>	<PathToChainFile>
+anoCar1	galGal3	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+anoCar1	gasAcu1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
+anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
+anoCar1	mm8	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToMm8.over.chain
+anoCar1	mm9	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToMm9.over.chain
+anoCar1	ornAna1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToOrnAna1.over.chain
+anoCar1	xenTro2	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToXenTro2.over.chain
+anoGam1	dm2	/depot/data2/galaxy/anoGam1/liftOver/anoGam1ToDm2.over.chain
+anoGam1	dm3	/depot/data2/galaxy/anoGam1/liftOver/anoGam1ToDm3.over.chain
+apiMel1	dm2	/depot/data2/galaxy/apiMel1/liftOver/apiMel1ToDm2.over.chain
+apiMel2	dm2	/depot/data2/galaxy/apiMel2/liftOver/apiMel2ToDm2.over.chain
+bosTau2	bosTau3	/depot/data2/galaxy/bosTau2/liftOver/bosTau2ToBosTau3.over.chain
+bosTau2	hg17	/depot/data2/galaxy/bosTau2/liftOver/bosTau2ToHg17.over.chain
+bosTau2	hg18	/depot/data2/galaxy/bosTau2/liftOver/bosTau2ToHg18.over.chain
+bosTau2	mm7	/depot/data2/galaxy/bosTau2/liftOver/bosTau2ToMm7.over.chain
+bosTau2	mm8	/depot/data2/galaxy/bosTau2/liftOver/bosTau2ToMm8.over.chain
+bosTau2	rn4	/depot/data2/galaxy/bosTau2/liftOver/bosTau2ToRn4.over.chain
+canFam1	canFam2	/depot/data2/galaxy/canFam1/liftOver/canFam1ToCanFam2.over.chain
+canFam1	hg17	/depot/data2/galaxy/canFam1/liftOver/canFam1ToHg17.over.chain
+canFam1	mm5	/depot/data2/galaxy/canFam1/liftOver/canFam1ToMm5.over.chain
+canFam1	mm6	/depot/data2/galaxy/canFam1/liftOver/canFam1ToMm6.over.chain
+canFam2	equCab1	/depot/data2/galaxy/canFam2/liftOver/canFam2ToEquCab1.over.chain
+canFam2	hg17	/depot/data2/galaxy/canFam2/liftOver/canFam2ToHg17.over.chain
+canFam2	hg18	/depot/data2/galaxy/canFam2/liftOver/canFam2ToHg18.over.chain
+canFam2	mm6	/depot/data2/galaxy/canFam2/liftOver/canFam2ToMm6.over.chain
+canFam2	mm7	/depot/data2/galaxy/canFam2/liftOver/canFam2ToMm7.over.chain
+canFam2	mm8	/depot/data2/galaxy/canFam2/liftOver/canFam2ToMm8.over.chain
+canFam2	mm9	/depot/data2/galaxy/canFam2/liftOver/canFam2ToMm9.over.chain
+canFam2	rn3	/depot/data2/galaxy/canFam2/liftOver/canFam2ToRn3.over.chain
+canFam2	rn4	/depot/data2/galaxy/canFam2/liftOver/canFam2ToRn4.over.chain
+ce2	ce4	/depot/data2/galaxy/ce2/liftOver/ce2ToCe4.over.chain
+ce4	caePb1	/depot/data2/galaxy/ce4/liftOver/ce4ToCaePb1.over.chain
+ce4	caeRem2	/depot/data2/galaxy/ce4/liftOver/ce4ToCaeRem2.over.chain
+ce4	cb3	/depot/data2/galaxy/ce4/liftOver/ce4ToCb3.over.chain
+ce4	priPac1	/depot/data2/galaxy/ce4/liftOver/ce4ToPriPac1.over.chain
\ No newline at end of file
diff --git a/tool-data/quality_scores.loc.sample b/tool-data/quality_scores.loc.sample
index fde5f839f86..68f2b7f52dd 100644
--- a/tool-data/quality_scores.loc.sample
+++ b/tool-data/quality_scores.loc.sample
@@ -4,6 +4,6 @@
 #
 #<build>	<QualityScoreDirectoryPath>
 #
-panTro2	/depot/data2/galaxy/quality_scores/panTro2
-rheMac2	/depot/data2/galaxy/quality_scores/rheMac2
-ponAbe2	/depot/data2/galaxy/quality_scores/ponAbe2
+panTro2	/depot/data2/galaxy/panTro2/quality_scores
+rheMac2	/depot/data2/galaxy/rheMac2/quality_scores
+ponAbe2	/depot/data2/galaxy/ponAbe2/quality_scores
diff --git a/tools/data_source/encode_import.py b/tools/data_source/encode_import.py
index 15aa5771c0a..74156dbea24 100755
--- a/tools/data_source/encode_import.py
+++ b/tools/data_source/encode_import.py
@@ -16,7 +16,7 @@ def stop_err( msg ):
 def main():
     uids = sys.argv[1].split(",")
     out_file1 = sys.argv[2]
-    file_name = "/depot/data2/galaxy/encode_datasets.loc"
+    file_name = "%s/encode_datasets.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
     
     #remove NONE from uids
     have_none = True
@@ -29,7 +29,7 @@ def main():
     #create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files
     available_files = {}
     try:
-        for line in open( file_name ):
+        for i, line in enumerate( file ( file_name ) ):
             line = line.rstrip( '\r\n' )
             if line and not line.startswith( '#' ):
                 fields = line.split( '\t' )
diff --git a/tools/data_source/encode_import_all_latest_datasets.xml b/tools/data_source/encode_import_all_latest_datasets.xml
index 7d5042a5b46..1044a237981 100644
--- a/tools/data_source/encode_import_all_latest_datasets.xml
+++ b/tools/data_source/encode_import_all_latest_datasets.xml
@@ -6,13 +6,13 @@
       <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
     </display>
     <param name="hg17" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="ALD" />
         <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="ALD" />
         <filter type="param" name="dbkey" value="hg16" />
       </options>
diff --git a/tools/data_source/encode_import_chromatin_and_chromosomes.xml b/tools/data_source/encode_import_chromatin_and_chromosomes.xml
index 643fe335937..a241e1f3e78 100644
--- a/tools/data_source/encode_import_chromatin_and_chromosomes.xml
+++ b/tools/data_source/encode_import_chromatin_and_chromosomes.xml
@@ -6,13 +6,13 @@
       <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
     </display>
     <param name="hg17" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="CC" />
         <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="CC" />
         <filter type="param" name="dbkey" value="hg16" />
       </options>
diff --git a/tools/data_source/encode_import_gencode.xml b/tools/data_source/encode_import_gencode.xml
index 2be284c36ed..5412aa6e3af 100644
--- a/tools/data_source/encode_import_gencode.xml
+++ b/tools/data_source/encode_import_gencode.xml
@@ -6,13 +6,13 @@
       <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
     </display>
     <param name="hg17" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="GENCODE" />
         <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="GENCODE" />
         <filter type="param" name="dbkey" value="hg16" />
       </options>
diff --git a/tools/data_source/encode_import_genes_and_transcripts.xml b/tools/data_source/encode_import_genes_and_transcripts.xml
index 489a8c952d2..9e13f3b5768 100644
--- a/tools/data_source/encode_import_genes_and_transcripts.xml
+++ b/tools/data_source/encode_import_genes_and_transcripts.xml
@@ -6,13 +6,13 @@
       <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
     </display>
     <param name="hg17" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="GT" />
         <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="GT" />
         <filter type="param" name="dbkey" value="hg16" />
       </options>
diff --git a/tools/data_source/encode_import_multi-species_sequence_analysis.xml b/tools/data_source/encode_import_multi-species_sequence_analysis.xml
index 7b518eb544b..4f687d8a81f 100644
--- a/tools/data_source/encode_import_multi-species_sequence_analysis.xml
+++ b/tools/data_source/encode_import_multi-species_sequence_analysis.xml
@@ -6,13 +6,13 @@
       <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
     </display>
     <param name="hg17" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="MSA" />
         <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="MSA" />
         <filter type="param" name="dbkey" value="hg16" />
       </options>
diff --git a/tools/data_source/encode_import_transcription_regulation.xml b/tools/data_source/encode_import_transcription_regulation.xml
index bfea84c1e81..20e03a1ad4c 100644
--- a/tools/data_source/encode_import_transcription_regulation.xml
+++ b/tools/data_source/encode_import_transcription_regulation.xml
@@ -6,13 +6,13 @@
       <p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
     </display>
     <param name="hg17" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="TR" />
         <filter type="param" name="dbkey" value="hg17" />
       </options>
     </param> 
     <param name="hg16" type="select" display="checkboxes" multiple="true">
-      <options from_file="/depot/data2/galaxy/encode_datasets.loc">
+      <options from_file="encode_datasets.loc">
         <filter type="param" name="encode_group" value="TR" />
         <filter type="param" name="dbkey" value="hg16" />
       </options>
diff --git a/tools/data_source/microbial_import.py b/tools/data_source/microbial_import.py
index 735eed94929..fb8fc26723c 100644
--- a/tools/data_source/microbial_import.py
+++ b/tools/data_source/microbial_import.py
@@ -24,7 +24,8 @@ while have_none:
 #create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files
 available_files = {}
 try:
-    for line in open( "/depot/data2/galaxy/microbes/microbial_data.loc" ):
+    filename = "%s/microbial_data.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
+    for i, line in enumerate( file( filename ) ):
         if not line or line[0:1] == "#" : continue
         fields = line.split('\t')
         try:
diff --git a/tools/data_source/microbial_import.xml b/tools/data_source/microbial_import.xml
index 5e616fd45b9..8534f8079bb 100644
--- a/tools/data_source/microbial_import.xml
+++ b/tools/data_source/microbial_import.xml
@@ -6,7 +6,7 @@
         <p><div class="toolFormTitle">Select the Desired Kingdom</div>$kingdom</p>
       </display>
       <param name="kingdom" type="select" display="radio">
-        <options from_file="/depot/data2/galaxy/microbes/microbial_data.loc" />
+        <options from_file="microbial_data.loc" />
       </param>
     </page>
     <page>
@@ -14,7 +14,7 @@
         <p><div class="toolFormTitle">Select the Desired Organism</div>$org</p>
       </display>
       <param name="org" type="select" display="radio">
-        <options from_file="/depot/data2/galaxy/microbes/microbial_data.loc">
+        <options from_file="microbial_data.loc">
           <filter type="param_value" name="kingdom" value="kingdom" />
         </options>
       </param>
@@ -30,49 +30,49 @@
         <p><div class="toolFormTitle">Select Desired Glimmer3 Annotations</div>$Glimmer3</p>
       </display>
       <param name="CDS" type="select" display="checkboxes" multiple="True">
-        <options from_file="/depot/data2/galaxy/microbes/microbial_data.loc">
+        <options from_file="microbial_data.loc">
           <filter type="param_value" name="kingdom" value="kingdom" />
           <filter type="param_value" name="org" value="org" />
           <filter type="param" name="feature" value="CDS" />
         </options>
       </param>
       <param name="tRNA" type="select" display="checkboxes" multiple="True">
-        <options from_file="/depot/data2/galaxy/microbes/microbial_data.loc">
+        <options from_file="microbial_data.loc">
           <filter type="param_value" name="kingdom" value="kingdom" />
           <filter type="param_value" name="org" value="org" />
           <filter type="param" name="feature" value="tRNA" />
         </options>
       </param>
       <param name="rRNA" type="select" display="checkboxes" multiple="True">
-        <options from_file="/depot/data2/galaxy/microbes/microbial_data.loc">
+        <options from_file="microbial_data.loc">
           <filter type="param_value" name="kingdom" value="kingdom" />
           <filter type="param_value" name="org" value="org" />
           <filter type="param" name="feature" value="rRNA" />
         </options>
       </param>
       <param name="sequence" type="select" display="checkboxes" multiple="True">
-        <options from_file="/depot/data2/galaxy/microbes/microbial_data.loc">
+        <options from_file="microbial_data.loc">
           <filter type="param_value" name="kingdom" value="kingdom" />
           <filter type="param_value" name="org" value="org" />
           <filter type="param" name="feature" value="sequence" />
         </options>
       </param>
       <param name="GeneMark" type="select" display="checkboxes" multiple="True">
-        <options from_file="/depot/data2/galaxy/microbes/microbial_data.loc">
+        <options from_file="microbial_data.loc">
           <filter type="param_value" name="kingdom" value="kingdom" />
           <filter type="param_value" name="org" value="org" />
           <filter type="param" name="feature" value="GeneMark" />
         </options>
       </param>
       <param name="GeneMarkHMM" type="select" display="checkboxes" multiple="True">
-        <options from_file="/depot/data2/galaxy/microbes/microbial_data.loc">
+        <options from_file="microbial_data.loc">
           <filter type="param_value" name="kingdom" value="kingdom" />
           <filter type="param_value" name="org" value="org" />
           <filter type="param" name="feature" value="GeneMarkHMM" />
         </options>
       </param>
       <param name="Glimmer3" type="select" display="checkboxes" multiple="True">
-        <options from_file="/depot/data2/galaxy/microbes/microbial_data.loc">
+        <options from_file="microbial_data.loc">
           <filter type="param_value" name="kingdom" value="kingdom" />
           <filter type="param_value" name="org" value="org" />
           <filter type="param" name="feature" value="Glimmer3" />
diff --git a/tools/data_source/microbial_import_code.py b/tools/data_source/microbial_import_code.py
index 6706396f206..1e99ec669ea 100644
--- a/tools/data_source/microbial_import_code.py
+++ b/tools/data_source/microbial_import_code.py
@@ -4,7 +4,9 @@ def load_microbial_data( sep='\t' ):
     # set data.name in exec_after_process(). 
     microbe_info= {}
     orgs = {}
-    for line in open( "/depot/data2/galaxy/microbes/microbial_data.loc" ):
+    
+    filename = "%s/microbial_data.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
+    for i, line in enumerate( file( filename ) ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( '#' ):
             fields = line.split( sep )
diff --git a/tools/encode/random_intervals.xml b/tools/encode/random_intervals.xml
index b919c414a04..620cd90c4ac 100644
--- a/tools/encode/random_intervals.xml
+++ b/tools/encode/random_intervals.xml
@@ -16,7 +16,7 @@
       <option value="none">None</option>
     </param>
     <param name="regions" type="select" label="Regions to use">
-      <options from_file="/depot/data2/galaxy/regions.loc" name_col="2" value_col="1">
+      <options from_file="regions.loc" name_col="2" value_col="1">
         <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="0" />
       </options>
     </param> 
diff --git a/tools/encode/random_intervals_no_bits.py b/tools/encode/random_intervals_no_bits.py
index c6aea8a2c61..4c07f68124f 100644
--- a/tools/encode/random_intervals_no_bits.py
+++ b/tools/encode/random_intervals_no_bits.py
@@ -106,7 +106,7 @@ def main():
         use_mask = sys.argv[11]
         overlaps = sys.argv[12]
     available_regions = {}
-    loc_file = "/depot/data2/galaxy/regions.loc"
+    loc_file = "%s/regions.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
     
     for i, line in enumerate( file( loc_file ) ):
         line = line.rstrip( '\r\n' )
diff --git a/tools/extract/extractAxt_wrapper.pl b/tools/extract/extractAxt_wrapper.pl
index f83bf7f2d98..e910293301a 100644
--- a/tools/extract/extractAxt_wrapper.pl
+++ b/tools/extract/extractAxt_wrapper.pl
@@ -5,7 +5,7 @@
 # directory of universe's tools section
 # Takes the following parameters:
 # extractorAxt_wrapper.pl -i $inp_file1 -o $out_file1 --species $species -g $dbkey $chroCol $startCol $endCol $strandCol
-# Location of alignment files is taken from /depot/data2/galaxy/alignseq.loc (to change -> edit line 19)
+# Location of alignment files is taken from $GALAXY_DATA_INDEX_DIR/alignseq.loc (to change -> edit line 19)
 
 use strict;
 use warnings;
@@ -16,7 +16,7 @@ die "Your query genome, $ARGV[7], is the same as your target genome, $ARGV[5]. P
 
 die "Not enough params -> check\n" unless @ARGV == 12;
 
-my $alignseqLoc = "/depot/data2/galaxy/alignseq.loc";
+my $alignseqLoc = "$GALAXY_DATA_INDEX_DIR/alignseq.loc";
 my %alignLocation = ();
 my @locFields = ();
 my $extractAxtStatus = 0;
diff --git a/tools/extract/extractAxt_wrapper.xml b/tools/extract/extractAxt_wrapper.xml
index d800ca72245..10ba5edf2b4 100644
--- a/tools/extract/extractAxt_wrapper.xml
+++ b/tools/extract/extractAxt_wrapper.xml
@@ -5,7 +5,7 @@
     <param format="interval" name="input" type="data" label="Between regions of Query"/>    
     <param name="species" type="select" label="and one of these genomes">
       <validator type="unspecified_build" />
-      <options from_file="/depot/data2/galaxy/alignseq.loc" name_col="1" value_col="2">
+      <options from_file="alignseq.loc" name_col="1" value_col="2">
         <filter type="data_meta" data_ref="input" meta_key="dbkey" meta_key_col="0" />
       </options>
     </param>    
diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/extract_genomic_dna.py
index 816343ee3a1..9eae9414de6 100644
--- a/tools/extract/extract_genomic_dna.py
+++ b/tools/extract/extract_genomic_dna.py
@@ -10,8 +10,8 @@ from bx.cookbook import doc_optparse
 import bx.seq.nib
 import bx.seq.twobit
 
-nib_file = "/depot/data2/galaxy/alignseq.loc"
-twobit_file = "/depot/data2/galaxy/twobit.loc"
+nib_file = "%s/alignseq.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
+twobit_file = "%s/twobit.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
 
 def stop_err( msg ):
     sys.stderr.write( msg )
diff --git a/tools/extract/extract_genomic_dna.xml b/tools/extract/extract_genomic_dna.xml
index 13b1d569318..465038be13c 100644
--- a/tools/extract/extract_genomic_dna.xml
+++ b/tools/extract/extract_genomic_dna.xml
@@ -3,7 +3,8 @@
   <command interpreter="python">extract_genomic_dna.py $input $out_file1 $input_chromCol $input_startCol $input_endCol $input_strandCol $dbkey $out_format</command>
   <inputs>
     <param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query">
-    <validator type="dataset_metadata_in_file" filename="/depot/data2/galaxy/alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Unspecified build (click the pencil icon in the history item) or sequences are not available for the build specified (you may request them via email)." split=" " line_startswith="seq"  />
+      <validator type="unspecified_build" />
+      <validator type="dataset_metadata_in_file" filename="alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." split=" " line_startswith="seq"  />
     </param>
 	<param name="out_format" type="select" label="Output data type">
 	<option value="fasta">FASTA</option>
diff --git a/tools/extract/liftOver_wrapper.py b/tools/extract/liftOver_wrapper.py
index 94117835a65..142f56d932f 100644
--- a/tools/extract/liftOver_wrapper.py
+++ b/tools/extract/liftOver_wrapper.py
@@ -21,7 +21,7 @@ mapfilepath = sys.argv[5]
 
 #ensure dbkey is set
 if in_dbkey == "?": 
-    stop_err( "Input dataset genome build unspecified, click the pencil icon in hte history item to specify it." )
+    stop_err( "Input dataset genome build unspecified, click the pencil icon in the history item to specify it." )
 
 cmd_line = "liftOver " + infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + "  > /dev/null 2>&1"
 
diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver_wrapper.xml
index 4d0df852098..be28b2e90a2 100644
--- a/tools/extract/liftOver_wrapper.xml
+++ b/tools/extract/liftOver_wrapper.xml
@@ -6,7 +6,7 @@
       <validator type="unspecified_build" />
     </param>
     <param name="to_dbkey" type="select" label="To">
-      <options from_file="/depot/data2/galaxy/liftOver.loc" name_col="1" value_col="2">
+      <options from_file="liftOver.loc" name_col="1" value_col="2">
         <filter type="data_meta" data_ref="input" meta_key="dbkey" meta_key_col="0"/>
       </options>
     </param> 
diff --git a/tools/extract/phastOdds/phastOdds_tool.xml b/tools/extract/phastOdds/phastOdds_tool.xml
index aba6314324f..25dc09e9cbc 100644
--- a/tools/extract/phastOdds/phastOdds_tool.xml
+++ b/tools/extract/phastOdds/phastOdds_tool.xml
@@ -6,7 +6,7 @@
       <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg17. Click the pencil icon in your history item to set the genome build."/>
     </param>
     <param name="score_file" type="select" label="Available datasets">
-      <options from_file="/depot/data2/galaxy/phastOdds.loc" name_col="1" value_col="2">
+      <options from_file="phastOdds.loc" name_col="1" value_col="2">
         <filter type="data_meta" data_ref="input" meta_key="dbkey" meta_key_col="0"/>
       </options>
     </param> 
diff --git a/tools/filters/axt_to_lav.xml b/tools/filters/axt_to_lav.xml
index 747cca001f4..2019667362b 100644
--- a/tools/filters/axt_to_lav.xml
+++ b/tools/filters/axt_to_lav.xml
@@ -1,7 +1,7 @@
 <tool id="axt_to_lav_1" name="AXT to LAV">
   <description>Converts an AXT formated file to LAV format</description>
   <!--  <command interpreter="python2.4">axt_to_lav.py $align_input $dbkey_1 $dbkey_2 $lav_file $seq_file1 $seq_file2</command> -->
-  <command interpreter="python2.4">axt_to_lav.py /depot/data2/galaxy/$dbkey_1/seq/%s.nib:$dbkey_1:./static/ucsc/chrom/${dbkey_1}.len /depot/data2/galaxy/$dbkey_2/seq/%s.nib:$dbkey_2:./static/ucsc/chrom/${dbkey_2}.len $align_input $lav_file $seq_file1 $seq_file2</command>
+  <command interpreter="python2.4">axt_to_lav.py ${GALAXY_DATA_INDEX_DIR}/$dbkey_1/seq/%s.nib:$dbkey_1:./static/ucsc/chrom/${dbkey_1}.len ${GALAXY_DATA_INDEX_DIR}/$dbkey_2/seq/%s.nib:$dbkey_2:./static/ucsc/chrom/${dbkey_2}.len $align_input $lav_file $seq_file1 $seq_file2</command>
   <inputs>
     <param name="align_input" type="data" format="axt" label="Alignment File" optional="False"/>
     <param name="dbkey_1" type="select" label="Genome">
diff --git a/tools/maf/genebed_maf_to_fasta.xml b/tools/maf/genebed_maf_to_fasta.xml
index 61a56313b27..ee67d245c23 100644
--- a/tools/maf/genebed_maf_to_fasta.xml
+++ b/tools/maf/genebed_maf_to_fasta.xml
@@ -26,13 +26,13 @@
       </when>
       <when value="cached">
         <param name="maf_identifier" type="select" label="MAF Type" >
-          <options from_file="/depot/data2/galaxy/maf_index.loc" name_col="0" value_col="1">
+          <options from_file="maf_index.loc" name_col="0" value_col="1">
             <validator type="no_options" message="No alignments are available for the build associated with the selected gene bed file"/>
             <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="2"/>
           </options>
         </param> 
         <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
-          <options from_file="/depot/data2/galaxy/maf_index.loc">
+          <options from_file="maf_index.loc">
             <filter type="param_meta" param_ref="maf_identifier" />
             <filter type="param" name="maf_source" value="cached" />
           </options>
diff --git a/tools/maf/interval2maf.xml b/tools/maf/interval2maf.xml
index 8d1dbd30cc1..a22c50bc79d 100644
--- a/tools/maf/interval2maf.xml
+++ b/tools/maf/interval2maf.xml
@@ -21,7 +21,7 @@
       </when>
       <when value="cached">
         <param name="mafType" type="select" label="Choose alignments">
-          <options from_file="/depot/data2/galaxy/maf_index.loc" name_col="0" value_col="1">
+          <options from_file="maf_index.loc" name_col="0" value_col="1">
             <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
             <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="2"/>
           </options>
diff --git a/tools/maf/interval2maf_pairwise.xml b/tools/maf/interval2maf_pairwise.xml
index 83277e5e5e6..d46c4c01e6c 100644
--- a/tools/maf/interval2maf_pairwise.xml
+++ b/tools/maf/interval2maf_pairwise.xml
@@ -1,12 +1,12 @@
 <tool id="Interval2Maf_pairwise1" name="Extract Pairwise MAF blocks">
   <description>given a set of genomic intervals</description>
-  <command interpreter="python2.4">interval2maf.py --dbkey=$input1_dbkey --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafType=$mafType --interval_file=$input1 --output_file=$out_file1 --indexLocation=/depot/data2/galaxy/maf_pairwise.loc</command>
+  <command interpreter="python2.4">interval2maf.py --dbkey=$input1_dbkey --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafType=$mafType --interval_file=$input1 --output_file=$out_file1 --indexLocation=${GALAXY_DATA_INDEX_DIR}/maf_pairwise.loc</command>
   <inputs>
     <param name="input1" type="data" format="interval" label="Interval File">
       <validator type="unspecified_build" />
     </param>
     <param name="mafType" type="select" label="Choose MAF source">
-      <options from_file="/depot/data2/galaxy/maf_pairwise.loc" name_col="0" value_col="1">
+      <options from_file="maf_pairwise.loc" name_col="0" value_col="1">
         <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
         <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="2"/>
       </options>
diff --git a/tools/maf/interval_maf_to_merged_fasta.xml b/tools/maf/interval_maf_to_merged_fasta.xml
index 7aac378c709..8c12799608c 100644
--- a/tools/maf/interval_maf_to_merged_fasta.xml
+++ b/tools/maf/interval_maf_to_merged_fasta.xml
@@ -27,13 +27,13 @@
             </when>
             <when value="cached">
               <param name="maf_identifier" type="select" label="MAF Type" >
-                <options from_file="/depot/data2/galaxy/maf_index.loc" name_col="0" value_col="1">
+                <options from_file="maf_index.loc" name_col="0" value_col="1">
                   <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
                   <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="2"/>
                 </options>
               </param> 
               <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
-                <options from_file="/depot/data2/galaxy/maf_index.loc">
+                <options from_file="maf_index.loc">
                   <filter type="param_meta" param_ref="maf_identifier" />
                   <filter type="param" name="maf_source" value="cached" />
                 </options>
diff --git a/tools/maf/maf_stats.xml b/tools/maf/maf_stats.xml
index 21b50909cc3..2150332838a 100644
--- a/tools/maf/maf_stats.xml
+++ b/tools/maf/maf_stats.xml
@@ -24,7 +24,7 @@
       </when>
       <when value="cached">
         <param name="mafType" type="select" label="MAF Type">
-          <options from_file="/depot/data2/galaxy/maf_index.loc" name_col="0" value_col="1">
+          <options from_file="maf_index.loc" name_col="0" value_col="1">
             <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
             <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="2"/>
           </options>
diff --git a/tools/maf/maf_stats_code.py b/tools/maf/maf_stats_code.py
index 2a6c233d322..7254187e07f 100644
--- a/tools/maf/maf_stats_code.py
+++ b/tools/maf/maf_stats_code.py
@@ -1,9 +1,11 @@
+import os
 
 def load_maf_data( sep='\t' ):
     # FIXME: this function is duplicated in the DynamicOptions class.  It is used here only to
     # set data.name in exec_before_job(). 
     maf_sets = {}
-    for line in open( "/depot/data2/galaxy/maf_index.loc" ):
+    filename = "%s/maf_index.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
+    for i, line in enumerate( file( filename ) ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( '#' ):
             fields = line.split( sep )
diff --git a/tools/metag_tools/blat_wrapper.py b/tools/metag_tools/blat_wrapper.py
index bbf301bb2a5..7996c8f2a50 100644
--- a/tools/metag_tools/blat_wrapper.py
+++ b/tools/metag_tools/blat_wrapper.py
@@ -2,13 +2,13 @@
 
 import os, sys, tempfile
 
-nib_file = "/depot/data2/galaxy/alignseq.loc"
-twobit_file = "/depot/data2/galaxy/twobit.loc"
+nib_file = "%s/alignseq.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
+twobit_file = "/%s/twobit.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
 
 def check_nib_file( dbkey ):
     nib_path = ''
     nibs = {}
-    for line in open( nib_file ):
+    for i, line in enumerate( file( nib_file ) ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( "#" ):
             fields = line.split()
@@ -23,7 +23,7 @@ def check_nib_file( dbkey ):
 def check_twobit_file( dbkey ):
     twobit_path = ''
     twobits = {}
-    for line in open( twobit_file ):
+    for i, line in enumerate( file( twobit_file ) ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( "#" ): 
             fields = line.split()
diff --git a/tools/metag_tools/megablast_wrapper.py b/tools/metag_tools/megablast_wrapper.py
index fbe4eb4467f..6a0db3982c7 100644
--- a/tools/metag_tools/megablast_wrapper.py
+++ b/tools/metag_tools/megablast_wrapper.py
@@ -6,7 +6,7 @@ run megablast for metagenomics data
 import sys, os, tempfile, subprocess
 from megablast_xml_parser import *
 
-DB_LOC = "/depot/data2/galaxy/blastdb.loc"
+DB_LOC = "%s/blastdb.loc" % os.environ.get( 'GALAXY_DATA_INDEX_DIR' )
 
 def __main__():
     # file I/O
diff --git a/tools/regVariation/quality_filter.xml b/tools/regVariation/quality_filter.xml
index b99ffe672c6..b0401dbc91f 100644
--- a/tools/regVariation/quality_filter.xml
+++ b/tools/regVariation/quality_filter.xml
@@ -16,7 +16,7 @@
   	#else
   		${mask_region.length}
 	#end if
-  	"/depot/data2/galaxy/quality_scores.loc"
+  	${GALAXY_DATA_INDEX_DIR}/quality_scores.loc
   </command>
   <inputs>
     <param format="maf" name="input" type="data" label="Select data"/>
diff --git a/tools/stats/aggregate_binned_scores_in_intervals.xml b/tools/stats/aggregate_binned_scores_in_intervals.xml
index 3bab4584b09..8761b477828 100644
--- a/tools/stats/aggregate_binned_scores_in_intervals.xml
+++ b/tools/stats/aggregate_binned_scores_in_intervals.xml
@@ -16,7 +16,7 @@
       </param>
       <when value="cached">
         <param name="datasets" type="select" label="Available datasets" display="radio">
-          <options from_file="/depot/data2/galaxy/binned_scores.loc" name_col="1" value_col="2">
+          <options from_file="binned_scores.loc" name_col="1" value_col="2">
             <filter type="data_meta" data_ref="input1" meta_key="dbkey" meta_key_col="0"/>
           </options>
         </param>