diff --git a/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py b/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
new file mode 100644
index 00000000000..6efa10af143
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
@@ -0,0 +1,61 @@
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+import sys, logging
+
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) )
+User_table = Table( "galaxy_user", metadata, autoload=True )
+HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True )
+
+def boolean_false():
+   if migrate_engine.name == 'postgres' or migrate_engine.name == 'mysql':
+       return False
+   elif migrate_engine.name == 'sqlite':
+       return 0
+   else:
+       raise Exception( 'Unable to convert data for unknown database type: %s' % db )
+              
+def upgrade():
+    # Load existing tables
+    metadata.reflect()
+    # Add 2 indexes to the galaxy_user table
+    i = Index( 'ix_galaxy_user_deleted', User_table.c.deleted )
+    try:
+        i.create()
+    except Exception, e:
+        log.debug( "Adding index 'ix_galaxy_user_deleted' to galaxy_user table failed: %s" % ( str( e ) ) )
+    i = Index( 'ix_galaxy_user_purged', User_table.c.purged )
+    try:
+        i.create()
+    except Exception, e:
+        log.debug( "Adding index 'ix_galaxy_user_purged' to galaxy_user table failed: %s" % ( str( e ) ) )
+    # Set the default data in the galaxy_user table, but only for null values
+    cmd = "UPDATE galaxy_user SET deleted = %s WHERE deleted is null"
+    cmd = cmd % boolean_false()
+    try:
+        db_session.execute( cmd )
+    except Exception, e:
+        log.debug( "Setting default data for galaxy_user.deleted column failed: %s" % ( str( e ) ) )
+    cmd = "UPDATE galaxy_user SET purged = %s WHERE purged is null"
+    cmd = cmd % boolean_false()
+    try:
+        db_session.execute( cmd )
+    except Exception, e:
+        log.debug( "Setting default data for galaxy_user.purged column failed: %s" % ( str( e ) ) )
+    # Add 1 index to the history_dataset_association table
+    i = Index( 'ix_hda_copied_from_library_dataset_dataset_association_id', HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id )
+    try:
+        i.create()
+    except Exception, e:
+        log.debug( "Adding index 'ix_hda_copied_from_library_dataset_dataset_association_id' to history_dataset_association table failed: %s" % ( str( e ) ) )
+def downgrade():
+    pass
diff --git a/manage_db.sh b/manage_db.sh
index 3201862a21e..8e48b186927 100644
--- a/manage_db.sh
+++ b/manage_db.sh
@@ -1,4 +1,9 @@
 #!/bin/sh
 
+#######
+# NOTE: To downgrade to a specific version, use something like:
+# sh manage_db.sh downgrade --version=3
+#######
+
 cd `dirname $0`
 python -ES ./scripts/manage_db.py $@
diff --git a/templates/dataset/edit_attributes.mako b/templates/dataset/edit_attributes.mako
index 723bafcdf6d..f60f47b30de 100644
--- a/templates/dataset/edit_attributes.mako
+++ b/templates/dataset/edit_attributes.mako
@@ -6,12 +6,11 @@
 
 <%def name="datatype( dataset, datatypes )">
     <select name="datatype">
-        ## $datatypes.sort()
         %for ext in datatypes:
             %if dataset.ext == ext:
-                <option value="${ext}" selected="yes">${_(ext)}}</option>
+                <option value="${ext}" selected="yes">${_(ext)}</option>
             %else:
-                <option value="${ext}">${_(ext)}}</option>
+                <option value="${ext}">${_(ext)}</option>
             %endif
         %endfor
     </select>
diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 3d3b6ea8575..c1f37307c6b 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -10,14 +10,6 @@
     <tool file="data_source/encode_db.xml" />
     <tool file="data_source/epigraph_import.xml" />
   </section>
-  <section name="Get ENCODE Data" id="encode">
-    <tool file="data_source/encode_import_chromatin_and_chromosomes.xml"/>
-    <tool file="data_source/encode_import_genes_and_transcripts.xml"/>
-    <tool file="data_source/encode_import_multi-species_sequence_analysis.xml"/>
-    <tool file="data_source/encode_import_transcription_regulation.xml"/>
-    <tool file="data_source/encode_import_all_latest_datasets.xml" />
-    <tool file="data_source/encode_import_gencode.xml" />
-  </section>
   <section name="Send Data" id="send">
     <tool file="data_destination/epigraph.xml" />
   </section>
@@ -42,17 +34,6 @@
     <tool file="filters/headWrapper.xml" />
     <tool file="filters/tailWrapper.xml" />
   </section>
-  <section name="Filter and Sort" id="filter">
-    <tool file="stats/filtering.xml" />
-    <tool file="filters/sorter.xml" />
-    <tool file="filters/grep.xml" />
-  </section>
-  <section name="Join, Subtract and Group" id="group">
-    <tool file="filters/joiner.xml" />
-    <tool file="filters/compare.xml"/>
-    <tool file="new_operations/subtract_query.xml"/>
-    <tool file="stats/grouping.xml" />   
-  </section>
   <section name="Convert Formats" id="convert">
     <tool file="filters/bed2gff.xml" />
     <tool file="fasta_tools/fasta_to_tabular.xml" />
@@ -68,15 +49,21 @@
     <tool file="fasta_tools/fasta_to_tabular.xml" />
     <tool file="fasta_tools/tabular_to_fasta.xml" />
   </section>
+  <section name="Filter and Sort" id="filter">
+    <tool file="stats/filtering.xml" />
+    <tool file="filters/sorter.xml" />
+    <tool file="filters/grep.xml" />
+  </section>
+  <section name="Join, Subtract and Group" id="group">
+    <tool file="filters/joiner.xml" />
+    <tool file="filters/compare.xml"/>
+    <tool file="new_operations/subtract_query.xml"/>
+    <tool file="stats/grouping.xml" />   
+  </section>
   <section name="Extract Features" id="features">
     <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
     <tool file="extract/extract_GFF_Features.xml" />
   </section>
-  <!--  
-  <section name="Pattern-Matching" id="patmat">
-    <tool file="patmat/findcluster_mysql.xml" />
-  </section> 
-  -->
   <section name="Fetch Sequences" id="fetchSeq">
     <tool file="extract/extract_genomic_dna.xml" />
   </section>
@@ -149,13 +136,20 @@
     <tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
     <tool file="hyphy/hyphy_dnds_wrapper.xml" />
  </section>
- <section name="Taxonomy manipulation" id="tax_manipulation">
+ <section name="Metagenomic analyses" id="tax_manipulation">
     <tool file="taxonomy/gi2taxonomy.xml" />
     <tool file="taxonomy/t2t_report.xml" />
     <tool file="taxonomy/t2ps_wrapper.xml" />
     <tool file="taxonomy/find_diag_hits.xml" />
+    <tool file="taxonomy/lca.xml" />
     <tool file="taxonomy/poisson2test.xml" />
   </section>
+  <section name="Short Read Analysis" id="short_read_analysis">
+    <tool file="metag_tools/short_reads_figure_score.xml" />
+    <tool file="metag_tools/short_reads_trim_seq.xml" />
+    <tool file="metag_tools/megablast_wrapper.xml" />
+    <tool file="metag_tools/megablast_xml_parser.xml" /> 
+  </section>
   <section name="EMBOSS" id="EMBOSSLite">
     <tool file="emboss_5/emboss_antigenic.xml" />
     <tool file="emboss_5/emboss_backtranseq.xml" />
@@ -265,10 +259,4 @@
     <tool file="emboss_5/emboss_wordcount.xml" />
     <tool file="emboss_5/emboss_wordmatch.xml" /> 
   </section>
-  <section name="Short Read Analysis" id="short_read_analysis">
-    <tool file="metag_tools/short_reads_figure_score.xml" />
-    <tool file="metag_tools/short_reads_trim_seq.xml" />
-    <tool file="metag_tools/megablast_wrapper.xml" />
-    <tool file="metag_tools/megablast_xml_parser.xml" /> 
-  </section>
 </toolbox>