diff --git a/cron/updateucsc.sh.sample b/cron/updateucsc.sh.sample
index fa33d659d34..ff4350bbf43 100644
--- a/cron/updateucsc.sh.sample
+++ b/cron/updateucsc.sh.sample
@@ -1,6 +1,6 @@
 #!/bin/sh 
 #
-# Script to update UCSC static tables.  The idea is to update, but if
+# Script to update UCSC shared data tables.  The idea is to update, but if
 # the update fails, not replace current data/tables with error
 # messages.
 
@@ -9,49 +9,49 @@ GALAXY=/galaxy/path
 export PYTHONPATH=${GALAXY}/modules:${GALAXY}/eggs:${GALAXY}/lib
 
 # setup directories
-mkdir ${GALAXY}/static/ucsc/new
-mkdir ${GALAXY}/static/ucsc/chrom/new
+mkdir ${GALAXY}/tool-data/shared/ucsc/new
+mkdir ${GALAXY}/tool-data/shared/ucsc/chrom/new
 
 date
-echo "Updating UCSC static tables."
+echo "Updating UCSC shared data tables."
 
 # Try to build "builds.txt"
 echo "Updating builds.txt"
-python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/static/ucsc/new/builds.txt
+python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt
 if [ $? -eq 0 ]
 then
-    cp -uf ${GALAXY}/static/ucsc/new/builds.txt ${GALAXY}/static/ucsc/builds.txt
+    cp -uf ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt
 else
     echo "Failed to update builds.txt" >&2
 fi
 
 # Try to build ucsc_build_sites.txt
 echo "Updating ucsc_build_sites.txt"
-python ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/static/ucsc/new/ucsc_build_sites.txt
+python ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt
 if [ $? -eq 0 ]
 then
-    cp -uf ${GALAXY}/static/ucsc/new/ucsc_build_sites.txt ${GALAXY}/static/ucsc/ucsc_build_sites.txt
+    cp -uf ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt
 else
     echo "Failed to update builds.txt" >&2
 fi
 
 # Try to build chromInfo tables
 echo "Building chromInfo tables."
-python ${GALAXY}/cron/build_chrom_db.py ${GALAXY}/static/ucsc/chrom/new/ ${GALAXY}/static/ucsc/builds.txt
+python ${GALAXY}/cron/build_chrom_db.py ${GALAXY}/tool-data/shared/ucsc/chrom/new/ ${GALAXY}/tool-data/shared/ucsc/builds.txt
 if [ $? -eq 0 ]
 then
-    cp -uf ${GALAXY}/static/ucsc/chrom/new/*.len ${GALAXY}/static/ucsc/chrom/
+    cp -uf ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len ${GALAXY}/tool-data/shared/ucsc/chrom/
 else
     echo "Failed to update chromInfo tables." >&2
 fi
 
-rm -rf ${GALAXY}/static/ucsc/new
-rm -rf ${GALAXY}/static/ucsc/chrom/new
+rm -rf ${GALAXY}/tool-data/shared/ucsc/new
+rm -rf ${GALAXY}/tool-data/shared/ucsc/chrom/new
 echo "Update complete."
 
 #Perform Manual Additions here
 echo "Adding Manual Builds."
-python ${GALAXY}/cron/add_manual_builds.py ${GALAXY}/static/ucsc/manual_builds.txt ${GALAXY}/static/ucsc/builds.txt ${GALAXY}/static/ucsc/chrom/
+python ${GALAXY}/cron/add_manual_builds.py ${GALAXY}/tool-data/shared/ucsc/manual_builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt ${GALAXY}/tool-data/shared/ucsc/chrom/
 if [ $? -eq 0 ]
 then
     echo "Manual addition was successful."
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index a4e03dd5e3b..81b51f4f1f4 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -242,7 +242,10 @@ def get_gbrowse_sites_by_build(build):
 
 def read_dbnames(filename):
     """ Read build names from file """
-    db_names = []
+    class DBNames( list ):
+        default_value = "?"
+        default_name = "unspecified (?)"
+    db_names = DBNames()
     try:
         ucsc_builds = {}
         man_builds = [] #assume these are integers
@@ -276,15 +279,15 @@ def read_dbnames(filename):
             ucsc_builds[db_base].sort()
             ucsc_builds[db_base].reverse()
             ucsc_builds[db_base] = [(build, name) for build_rev, build, name in ucsc_builds[db_base]]
-            db_names = db_names + ucsc_builds[db_base]
-        if len(db_names)>1 and len(man_builds)>0: db_names.append(('?', '----- Additional Species Are Below -----'))
+            db_names = DBNames( db_names + ucsc_builds[db_base] )
+        if len( db_names ) > 1 and len( man_builds ) > 0: db_names.append( ( db_names.default_value, '----- Additional Species Are Below -----' ) )
         man_builds.sort()
         man_builds = [(build, name) for name, build  in man_builds]
-        db_names = db_names + man_builds
+        db_names = DBNames( db_names + man_builds )
     except Exception, e:
         print "ERROR: Unable to read builds file:", e
     if len(db_names)<1:
-        db_names = [('?', 'unspecified (?)')]
+        db_names = DBNames( [( db_names.default_value,  db_names.default_name )] )
     return db_names
 
 def read_build_sites(filename):
@@ -306,9 +309,9 @@ def read_build_sites(filename):
     return build_sites
 
 galaxy_root_path = os.path.join(__path__[0], "..","..","..")
-dbnames = read_dbnames(os.path.join(galaxy_root_path,"static","ucsc","builds.txt")) #this list is used in edit attributes and the upload tool
-ucsc_build_sites = read_build_sites(os.path.join(galaxy_root_path,"static","ucsc","ucsc_build_sites.txt")) #this list is used in history.tmpl
-gbrowse_build_sites = read_build_sites(os.path.join(galaxy_root_path,"static","gbrowse","gbrowse_build_sites.txt")) #this list is used in history.tmpl
+dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) ) #this list is used in edit attributes and the upload tool
+ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "ucsc_build_sites.txt" ) ) #this list is used in history.tmpl
+gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) ) #this list is used in history.tmpl
 
 if __name__ == '__main__':
     import doctest, sys
diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py
index 6e27916293e..6c3911c7a3a 100644
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -187,7 +187,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         initialize a new history with the first dbkey in util.dbnames which is currently
         ?    unspecified (?)
         """
-        history.genome_build = util.dbnames[0][0]
+        history.genome_build = util.dbnames.default_value
         if history.user_id is None and self.user is not None:
             history.user_id = self.user.id
         if self.galaxy_session_is_valid():
diff --git a/static/gbrowse/gbrowse_build_sites.txt b/tool-data/shared/gbrowse/gbrowse_build_sites.txt
similarity index 100%
rename from static/gbrowse/gbrowse_build_sites.txt
rename to tool-data/shared/gbrowse/gbrowse_build_sites.txt
diff --git a/static/ucsc/builds.txt b/tool-data/shared/ucsc/builds.txt
similarity index 100%
rename from static/ucsc/builds.txt
rename to tool-data/shared/ucsc/builds.txt
diff --git a/static/ucsc/manual_builds.txt b/tool-data/shared/ucsc/manual_builds.txt
similarity index 100%
rename from static/ucsc/manual_builds.txt
rename to tool-data/shared/ucsc/manual_builds.txt
diff --git a/static/ucsc/ucsc_build_sites.txt b/tool-data/shared/ucsc/ucsc_build_sites.txt
similarity index 100%
rename from static/ucsc/ucsc_build_sites.txt
rename to tool-data/shared/ucsc/ucsc_build_sites.txt
diff --git a/tools/annotation_profiler/annotation_profiler.xml b/tools/annotation_profiler/annotation_profiler.xml
index 95fb2294ca0..e297902ac63 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="python2.4">annotation_profiler_for_interval.py -i $input1 -c $input1_chromCol -s $input1_startCol -e $input1_endCol -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -b 3 -t $table_names</command>
+  <command interpreter="python2.4">annotation_profiler_for_interval.py -i $input1 -c $input1_chromCol -s $input1_startCol -e $input1_endCol -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len -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 f11edb55c6f..d6f33289f9f 100644
--- a/tools/annotation_profiler/annotation_profiler_for_interval.py
+++ b/tools/annotation_profiler/annotation_profiler_for_interval.py
@@ -111,8 +111,9 @@ class CachedCoverageReader:
             yield tablename, coverage, regions, index
 
 class TableCoverageSummary:
-    def __init__( self, coverage_reader ):
+    def __init__( self, coverage_reader, chrom_lengths ):
         self.coverage_reader = coverage_reader
+        self.chrom_lengths = chrom_lengths
         self.chromosome_coverage = {}
         self.total_interval_size = 0
         self.total_interval_count = 0
@@ -126,10 +127,7 @@ class TableCoverageSummary:
         self.total_interval_size += ( end - start )
         self.total_interval_count += 1
         if chrom not in self.chromosome_coverage:
-            #utilize lengths file here, if possible, if not use 250mb
-            #currently, no valid method to provide location of lengths file by framework:
-            #gops_complement has it hard coded as dbfile = fileinput.FileInput( "static/ucsc/chrom/"+db+".len" )
-            self.chromosome_coverage[chrom] = bx.bitset.BitSet( 250000000 )
+            self.chromosome_coverage[chrom] = bx.bitset.BitSet( self.chrom_lengths.get( chrom ) )
         self.chromosome_coverage[chrom].set_range( start, end - start )
         for table_name, coverage, regions in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, start, end ):
             if table_name not in self.table_coverage:
@@ -207,19 +205,34 @@ def profile_per_interval( interval_filename, chrom_col, start_col, end_col, out_
                 out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), table_name, coverage, region_count ) )
     out.close()
 
-def profile_summary( interval_filename, chrom_col, start_col, end_col, out_filename, keep_empty, coverage_reader ):
+def profile_summary( interval_filename, chrom_col, start_col, end_col, out_filename, keep_empty, coverage_reader, chrom_lengths ):
     out = open( out_filename, 'wb' )
-    table_coverage_summary = TableCoverageSummary( coverage_reader )
+    table_coverage_summary = TableCoverageSummary( coverage_reader, chrom_lengths )
     for region in bx.intervals.io.NiceReaderWrapper( open( interval_filename, 'rb' ), chrom_col = chrom_col, start_col = start_col, end_col = end_col, fix_strand = True, return_header = False, return_comments = False ):
         table_coverage_summary.add_region( region.chrom, region.start, region.end )
     
-    out.write( "#tableName\ttableChromosomeCoverage\ttableChromosomeCount\ttableRegionCoverage\ttableRegionCount\tallIntervalCount\tallIntervalSize\tallCoverage\tallTableRegionsOverlaped\tallIntervalsOverlapingTable\tnrIntervalCount\tnrIntervalSize\tnrCoverage\tnrTableRegionsOverlaped\tnrIntervalsOverlapingTable\n" )#\tstatistic\n" )
+    out.write( "#tableName\ttableChromosomeCoverage\ttableChromosomeCount\ttableRegionCoverage\ttableRegionCount\tallIntervalCount\tallIntervalSize\tallCoverage\tallTableRegionsOverlaped\tallIntervalsOverlapingTable\tnrIntervalCount\tnrIntervalSize\tnrCoverage\tnrTableRegionsOverlaped\tnrIntervalsOverlapingTable\n" )
     for table_name, table_chromosome_size, table_chromosome_count, table_region_coverage, table_region_count, total_interval_count, total_interval_size, total_coverage, table_regions_overlaped_count, interval_region_overlap_count, nr_interval_count, nr_region_size, nr_coverage, nr_table_regions_overlaped_count, nr_interval_table_overlap_count in table_coverage_summary.iter_table_coverage():
         if keep_empty or total_coverage:
             #only output tables that have atleast 1 base covered unless empty are requested
             out.write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( table_name, table_chromosome_size, table_chromosome_count, table_region_coverage, table_region_count, total_interval_count, total_interval_size, total_coverage, table_regions_overlaped_count, interval_region_overlap_count, nr_interval_count, nr_region_size, nr_coverage, nr_table_regions_overlaped_count, nr_interval_table_overlap_count ) )
     out.close()
 
+class ChromosomeLengths:
+    def __init__( self, filename ):
+        self.chroms = {}
+        try:
+            for line in open( filename ):
+                try:
+                    fields = line.strip().split( "\t" )
+                    self.chroms[fields[0]] = int( fields[1] )
+                except:
+                    continue
+        except:
+            pass
+    def get( self, name ):
+        return self.chroms.get( name, bx.bitset.MAX )
+
 def __main__():
     parser = optparse.OptionParser()
     parser.add_option(
@@ -259,6 +272,12 @@ def __main__():
         type='str',default='/depot/data2/galaxy/annotation_profiler/hg18',
         help='Path to profiled data for this organism'
     )
+    parser.add_option(
+        '-l','--lengths',
+        dest='lengths',
+        type='str',default='test-data/shared/ucsc/hg18.len',
+        help='Path to chromosome lengths data for this organism'
+    )
     parser.add_option(
         '-t','--table_names',
         dest='table_names',
@@ -292,7 +311,7 @@ def __main__():
     coverage_reader = CachedCoverageReader( options.path, buffer = options.buffer, table_names = table_names )
     
     if options.summary:
-        profile_summary( options.interval_filename, options.chrom_col - 1, options.start_col - 1, options.end_col -1, options.out_filename, options.keep_empty, coverage_reader )
+        profile_summary( options.interval_filename, options.chrom_col - 1, options.start_col - 1, options.end_col -1, options.out_filename, options.keep_empty, coverage_reader, ChromosomeLengths( options.lengths ) )
     else:
         profile_per_interval( options.interval_filename, options.chrom_col - 1, options.start_col - 1, options.end_col -1, options.out_filename, options.keep_empty, coverage_reader )
     
diff --git a/tools/filters/axt_to_lav.xml b/tools/filters/axt_to_lav.xml
index a693285b5b6..39c3b734240 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 formated file to LAV format</description>
-  <command interpreter="python">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 $seq_file2</command>
+  <command interpreter="python">axt_to_lav.py /depot/data2/galaxy/$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>
   <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/new_operations/complement.xml b/tools/new_operations/complement.xml
index 6a8b7d70715..cccde19e0f6 100644
--- a/tools/new_operations/complement.xml
+++ b/tools/new_operations/complement.xml
@@ -1,6 +1,6 @@
 <tool id="gops_complement_1" name="Complement">
   <description>intervals of a query</description>
-  <command interpreter="python">gops_complement.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -d $dbkey $allchroms</command>
+  <command interpreter="python">gops_complement.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len $allchroms</command>
   <inputs>
     <param format="interval" name="input1" type="data">
       <label>Complement regions of</label>
diff --git a/tools/new_operations/gops_complement.py b/tools/new_operations/gops_complement.py
index 09a78e25e51..7615f83f4e2 100644
--- a/tools/new_operations/gops_complement.py
+++ b/tools/new_operations/gops_complement.py
@@ -4,7 +4,7 @@ Complement regions.
 
 usage: %prog in_file out_file
     -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file
-    -d, --db=N: Database name (for determining chromosome lengths)
+    -l, --lengths=N: Filename of .len file for species (chromosome lengths)
     -a, --all: Complement all chromosomes (Genome-wide complement)
 """
 from galaxy import eggs
@@ -29,7 +29,7 @@ def main():
     options, args = doc_optparse.parse( __doc__ )
     try:
         chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
-        db = options.db
+        lengths = options.lengths
         if options.all: allchroms = True
         in_fname, out_fname = args
     except:
@@ -46,7 +46,7 @@ def main():
     chroms = list()
     # dbfile is used to determine the length of each chromosome.  The lengths
     # are added to the lens dict and passed copmlement operation code in bx.
-    dbfile = fileinput.FileInput( "static/ucsc/chrom/"+db+".len" )
+    dbfile = fileinput.FileInput( lengths )
     
     if dbfile:
         if not allchroms: