diff --git a/buildbot_setup.sh b/buildbot_setup.sh
index bbef942141e..3027754527e 100644
--- a/buildbot_setup.sh
+++ b/buildbot_setup.sh
@@ -26,6 +26,7 @@ esac
 
 LINKS="
 /galaxy/data/location/alignseq.loc
+/galaxy/data/annotation_profiler
 /galaxy/data/annotation_profiler/annotation_profiler.loc
 /galaxy/data/annotation_profiler/annotation_profiler_options.xml
 /galaxy/data/annotation_profiler/annotation_profiler_valid_builds.txt
@@ -45,7 +46,7 @@ LINKS="
 /galaxy/data/location/quality_scores.loc
 /galaxy/data/location/regions.loc
 /galaxy/data/location/sam_fa_indices.loc
-/galaxy/data/location/taxonomy
+/galaxy/data/taxonomy
 /galaxy/data/location/twobit.loc
 "
 
diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py
index 18d01391928..5be18286b7e 100644
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -1674,7 +1674,7 @@ class TwillTestCase( unittest.TestCase ):
             url += "&ldda_ids=%s" % ldda_id
         self.visit_url( url )
         tc.code( 200 )
-        archive = self.write_temp_file( self.last_page(), suffix=format )
+        archive = self.write_temp_file( self.last_page(), suffix='.' + format )
         self.home()
         return archive
     def check_archive_contents( self, archive, lddas ):
diff --git a/tools/annotation_profiler/annotation_profiler.xml b/tools/annotation_profiler/annotation_profiler.xml
index 1d5fbc3a58c..752d6aa7a35 100644
--- a/tools/annotation_profiler/annotation_profiler.xml
+++ b/tools/annotation_profiler/annotation_profiler.xml
@@ -1,6 +1,6 @@
 <tool id="Annotation_Profiler_0" name="Profile Annotations" Version="1.0.0">
   <description>for a set of genomic intervals</description>
-  <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${chromInfo} -b 3 -t $table_names</command>
+  <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p ${GALAXY_DATA_INDEX_DIR}/annotation_profiler/$dbkey $summary -l ${chromInfo} -b 3 -t $table_names</command>
   <inputs>
     <param format="interval" name="input1" type="data" label="Choose Intervals">
       <validator type="dataset_metadata_in_file" filename="annotation_profiler_valid_builds.txt" metadata_name="dbkey" metadata_column="0" message="Profiling is not currently available for this species."/>
diff --git a/tools/annotation_profiler/annotation_profiler_for_interval.py b/tools/annotation_profiler/annotation_profiler_for_interval.py
index a0939de2971..b427de1389a 100644
--- a/tools/annotation_profiler/annotation_profiler_for_interval.py
+++ b/tools/annotation_profiler/annotation_profiler_for_interval.py
@@ -290,7 +290,7 @@ def __main__():
     parser.add_option(
         '-p','--path',
         dest='path',
-        type='str',default='/depot/data2/galaxy/annotation_profiler/hg18',
+        type='str',default='/galaxy/data/annotation_profiler/hg18',
         help='Path to profiled data for this organism'
     )
     parser.add_option(
diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver_wrapper.xml
index cfabfa4eae2..28e3dcd4feb 100644
--- a/tools/extract/liftOver_wrapper.xml
+++ b/tools/extract/liftOver_wrapper.xml
@@ -27,7 +27,7 @@
   <tests>
     <test>
       <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
-      <param name="to_dbkey" value="/depot/data2/galaxy/hg18/liftOver/hg18ToPanTro2.over.chain" />
+      <param name="to_dbkey" value="/galaxy/data/hg18/liftOver/hg18ToPanTro2.over.chain" />
       <param name="minMatch" value="0.95" />
       <output name="out_file1" file="5_liftover_mapped.bed"/>
       <output name="out_file2" file="5_liftover_unmapped.bed"/>
diff --git a/tools/extract/phastOdds/phastOdds_tool.xml b/tools/extract/phastOdds/phastOdds_tool.xml
index 34d6bde909b..72883f04142 100644
--- a/tools/extract/phastOdds/phastOdds_tool.xml
+++ b/tools/extract/phastOdds/phastOdds_tool.xml
@@ -26,7 +26,7 @@
   <tests>
     <test>
       <param name="input" value="4.bed" dbkey="hg17" ftype="bed"/>
-      <param name="score_file" value="/depot/data2/galaxy/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds" />
+      <param name="score_file" value="/galaxy/data/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds" />
       <param name="per_col" value="true" />
       <output name="output" file="phastOdds_tool_out.interval" />
     </test>
diff --git a/tools/filters/axt_to_lav.xml b/tools/filters/axt_to_lav.xml
index 33adb210674..f2fc6971b33 100644
--- a/tools/filters/axt_to_lav.xml
+++ b/tools/filters/axt_to_lav.xml
@@ -1,6 +1,6 @@
 <tool id="axt_to_lav_1" name="AXT to LAV">
   <description>Converts an AXT formatted file to LAV format</description>
-  <command interpreter="python">axt_to_lav.py /depot/data2/galaxy/$dbkey_1/seq/%s.nib:$dbkey_1:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_1}.len /depot/data2/galaxy/$dbkey_2/seq/%s.nib:$dbkey_2:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_2}.len $align_input $lav_file $seq_file1 $seq_file2</command>
+  <command interpreter="python">axt_to_lav.py /galaxy/data/$dbkey_1/seq/%s.nib:$dbkey_1:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_1}.len /depot/data2/galaxy/$dbkey_2/seq/%s.nib:$dbkey_2:${GALAXY_DATA_INDEX_DIR}/shared/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="genomebuild" label="Genome"/>
diff --git a/tools/filters/lav_to_bed.xml b/tools/filters/lav_to_bed.xml
index 3063024f6f8..d04e2ac8022 100644
--- a/tools/filters/lav_to_bed.xml
+++ b/tools/filters/lav_to_bed.xml
@@ -33,8 +33,8 @@ This tool converts a LAV formatted file to the BED format.
 
     #:lav
     s {
-      &quot;/depot/data2/galaxy/hg16/seq/chr19.nib&quot; 1 63811651 0 1
-      &quot;/depot/data2/galaxy/mm5/seq/chr11.nib&quot; 1 121648857 0 1
+      &quot;/galaxy/data/hg16/seq/chr19.nib&quot; 1 63811651 0 1
+      &quot;/galaxy/data/mm5/seq/chr11.nib&quot; 1 121648857 0 1
     }
     h {
       &quot;> hg16.chr19&quot;
@@ -65,4 +65,4 @@ This tool converts a LAV formatted file to the BED format.
     chr11	70573975	70574054	mm5_1	0	+
   </help>
   <code file="lav_to_bed_code.py"/>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/metag_tools/rmap_wrapper.xml b/tools/metag_tools/rmap_wrapper.xml
index da2bf8044eb..36add8973ae 100644
--- a/tools/metag_tools/rmap_wrapper.xml
+++ b/tools/metag_tools/rmap_wrapper.xml
@@ -41,7 +41,7 @@
     <!--     
     <tests>
         <test>
-            <param name="database" value="/depot/data2/galaxy/faseq/test" />
+            <param name="database" value="/galaxy/data/faseq/test" />
             <param name="input_seq" value="rmap_wrapper_test1.fasta" ftype="fasta"/>
             <param name="read_len" value="36" />
             <param name="align_len" value="36" />
diff --git a/tools/metag_tools/rmapq_wrapper.xml b/tools/metag_tools/rmapq_wrapper.xml
index 2a02ba80c2a..8e7b74aed98 100644
--- a/tools/metag_tools/rmapq_wrapper.xml
+++ b/tools/metag_tools/rmapq_wrapper.xml
@@ -44,7 +44,7 @@
     <!-- 
     <tests>
         <test>
-            <param name="database" value="/depot/data2/galaxy/faseq/test" />
+            <param name="database" value="/galaxy/data/faseq/test" />
             <param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/>
             <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qualsolexa" />
             <param name="high_score" value="40" />
diff --git a/tools/samtools/sam_to_bam.py b/tools/samtools/sam_to_bam.py
index f11dba69e0c..c183c045598 100644
--- a/tools/samtools/sam_to_bam.py
+++ b/tools/samtools/sam_to_bam.py
@@ -45,14 +45,14 @@ def __main__():
     cached_seqs_pointer_file = '%s/sam_fa_indices.loc' % options.index_dir
     if not os.path.exists( cached_seqs_pointer_file ):
         stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file )
-    # If found for the dbkey, seq_path will look something like /depot/data2/galaxy/equCab2/sam_index/equCab2.fa,
+    # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa,
     # and the equCab2.fa file will contain fasta sequences.
     seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file )
     tmp_dir = tempfile.mkdtemp()
     if options.ref_file == 'None':
-        # We're using locally cached reference sequences( e.g., /depot/data2/galaxy/equCab2/sam_index/equCab2.fa ).
-        # The indexes for /depot/data2/galaxy/equCab2/sam_index/equCab2.fa will be contained in
-        # a file named /depot/data2/galaxy/equCab2/sam_index/equCab2.fa.fai
+        # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).
+        # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in
+        # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai
         fai_index_file_base = seq_path
         fai_index_file_path = '%s.fai' % seq_path 
         if not os.path.exists( fai_index_file_path ):
diff --git a/tools/stats/aggregate_binned_scores_in_intervals.xml b/tools/stats/aggregate_binned_scores_in_intervals.xml
index 8a0bc9147ed..ba466b51e91 100644
--- a/tools/stats/aggregate_binned_scores_in_intervals.xml
+++ b/tools/stats/aggregate_binned_scores_in_intervals.xml
@@ -42,13 +42,13 @@
     <test>
       <param name="input1" value="6.bed" dbkey="hg17" ftype="bed"/>
       <param name="score_source" value="cached"/>
-      <param name="datasets" value="/depot/data2/galaxy/binned_scores/hg17/phastcons_encode_sep2005_tba" />
+      <param name="datasets" value="/galaxy/data/binned_scores/hg17/phastcons_encode_sep2005_tba" />
       <output name="out_file1" file="aggregate_binned_scores_in_intervals.out" />
     </test>
     <test>
       <param name="input1" value="9_hg18.bed" dbkey="hg18" ftype="bed"/>
       <param name="score_source" value="cached"/>
-      <param name="datasets" value="/depot/data2/galaxy/binned_scores/hg18/phastCons17way/ba" />
+      <param name="datasets" value="/galaxy/data/binned_scores/hg18/phastCons17way/ba" />
       <output name="out_file1" file="aggregate_binned_scores_in_intervals2.interval" />
     </test>
     <test>