diff --git a/tool_collections/taxonomy/find_diag_hits/find_diag_hits.py b/tool_collections/taxonomy/find_diag_hits/find_diag_hits.py
index 0b6b7e22..d22cb880 100644
--- a/tool_collections/taxonomy/find_diag_hits/find_diag_hits.py
+++ b/tool_collections/taxonomy/find_diag_hits/find_diag_hits.py
@@ -136,7 +136,7 @@ def stop_err(msg):
         val_string = val_string.strip(', ')
         val_string = "insert into tax values(" + val_string + ")"
         cur.execute(val_string)
-except Exception, e:
+except Exception as e:
     stop_err('%s\n' % e)
 
 tax_file.close()    
@@ -165,6 +165,6 @@ def stop_err(msg):
                 out_string = '%s\t%s\t' % ( item[0], item[1] )
                 out_string += rankName
                 print >>out_file, out_string
-except Exception, e:
+except Exception as e:
     stop_err("%s\n" % e)
     
diff --git a/tool_collections/taxonomy/find_diag_hits/find_diag_hits.xml b/tool_collections/taxonomy/find_diag_hits/find_diag_hits.xml
index b02821fd..739df497 100644
--- a/tool_collections/taxonomy/find_diag_hits/find_diag_hits.xml
+++ b/tool_collections/taxonomy/find_diag_hits/find_diag_hits.xml
@@ -1,4 +1,4 @@
-<tool id="find_diag_hits" name="Find diagnostic hits" version="1.0.0">
+<tool id="find_diag_hits" name="Find diagnostic hits" version="1.0.1">
     <description></description>
     <requirements>
         <requirement type="package" version="1.0.0">taxonomy</requirement>
diff --git a/tool_collections/taxonomy/lca_wrapper/lca.py b/tool_collections/taxonomy/lca_wrapper/lca.py
index a1d9f1ca..dd349fff 100644
--- a/tool_collections/taxonomy/lca_wrapper/lca.py
+++ b/tool_collections/taxonomy/lca_wrapper/lca.py
@@ -65,7 +65,7 @@ class       :10,
         if POS2 is not specified, the newer versions of sort will consider the entire line for sorting. To prevent this, we set POS2=POS1.
         """
         command_line = "sort -f -k " + str(group_col+1) +"," + str(group_col+1) + " -o " + tmpfile.name + " " + inputfile
-    except Exception, exc:
+    except Exception as exc:
         stop_err( 'Initialization error -> %s' %str(exc) )
         
     error_code, stdout = commands.getstatusoutput(command_line)
@@ -190,4 +190,4 @@ class       :10,
         print "Skipped %d invalid lines." % ( skipped_lines )
     
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()
diff --git a/tool_collections/taxonomy/lca_wrapper/lca.xml b/tool_collections/taxonomy/lca_wrapper/lca.xml
index 11c3ac60..09656662 100644
--- a/tool_collections/taxonomy/lca_wrapper/lca.xml
+++ b/tool_collections/taxonomy/lca_wrapper/lca.xml
@@ -1,4 +1,4 @@
-<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.1">
+<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.2">
   <description></description>
     <requirements>
         <requirement type="package" version="1.0.0">taxonomy</requirement>
diff --git a/tool_collections/taxonomy/t2ps/t2ps.tgz b/tool_collections/taxonomy/t2ps/t2ps.tgz
deleted file mode 100644
index 09af4b33..00000000
Binary files a/tool_collections/taxonomy/t2ps/t2ps.tgz and /dev/null differ
diff --git a/tool_collections/taxonomy/t2ps/t2ps_wrapper.py b/tool_collections/taxonomy/t2ps/t2ps_wrapper.py
index cc1cf0f0..a96dce72 100644
--- a/tool_collections/taxonomy/t2ps/t2ps_wrapper.py
+++ b/tool_collections/taxonomy/t2ps/t2ps_wrapper.py
@@ -42,7 +42,7 @@ def stop_err(msg):
     retcode = subprocess.call( t2t_cmd, shell=True )
     if retcode < 0:
         print >>sys.stderr, "Execution of taxonomy2tree terminated by signal", -retcode
-except OSError, e:
+except OSError as e:
     print >>sys.stderr, "Execution of taxonomy2tree failed:", e
 
 
@@ -53,7 +53,7 @@ def stop_err(msg):
     retcode = subprocess.call( t2ps_cmd, shell=True )
     if retcode < 0:
         print >>sys.stderr, "Execution of tree2PS-fast terminated by signal", -retcode
-except OSError, e:
+except OSError as e:
     print >>sys.stderr, "Execution of tree2PS-fast failed:", e
     
 # Convert PS to PDF
@@ -63,5 +63,5 @@ def stop_err(msg):
     retcode = subprocess.call( ps2pdf_cmd, shell=True )
     if retcode < 0:
         print >>sys.stderr, "Execution of ps2pdf terminated by signal", -retcode
-except OSError, e:
+except OSError as e:
     print >>sys.stderr, "Execution of ps2pdf failed:", e
diff --git a/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml b/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml
index 7b651388..7ac4c648 100644
--- a/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml
+++ b/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="Draw_phylogram" name="Draw phylogeny" version="1.0.0">
+<tool id="Draw_phylogram" name="Draw phylogeny" version="1.0.1">
   <description></description>
     <requirements>
         <requirement type="package" version="1.0.0">taxonomy</requirement>
diff --git a/tools/annotation_profiler/annotation_profiler.xml b/tools/annotation_profiler/annotation_profiler.xml
index 3c38a54e..72a3f26b 100644
--- a/tools/annotation_profiler/annotation_profiler.xml
+++ b/tools/annotation_profiler/annotation_profiler.xml
@@ -1,4 +1,4 @@
-<tool id="Annotation_Profiler_0" name="Profile Annotations" version="1.0.0">
+<tool id="Annotation_Profiler_0" name="Profile Annotations" version="1.0.1">
   <description>for a set of genomic intervals</description>
   <requirements>
     <requirement type="package" version="0.7.1">bx-python</requirement>
diff --git a/tools/annotation_profiler/annotation_profiler_for_interval.py b/tools/annotation_profiler/annotation_profiler_for_interval.py
index 3445e7f3..a2e611af 100644
--- a/tools/annotation_profiler/annotation_profiler_for_interval.py
+++ b/tools/annotation_profiler/annotation_profiler_for_interval.py
@@ -34,7 +34,7 @@ def __getitem__( self, i ):
         try:
             start = struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0]
             end = struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0]
-        except Exception, e:
+        except Exception as e:
             raise IndexError, e
         self._cached_ranges[i] = ( start, end )
         return start, end
@@ -45,12 +45,12 @@ class RegionCoverage:
     def __init__( self, filename_base, profiler_info ):
         try:
             self._coverage = CachedRangesInFile( "%s.covered" % filename_base, profiler_info )
-        except Exception, e:
+        except Exception as e:
             #print "Error loading coverage file %s: %s" % ( "%s.covered" % filename_base, e )
             self._coverage = []
         try: 
             self._total_coverage = int( open( "%s.total_coverage" % filename_base ).read() )
-        except Exception, e:
+        except Exception as e:
             #print "Error loading total coverage file %s: %s" % ( "%s.total_coverage" % filename_base, e )
             self._total_coverage = 0
     def get_start_index( self, start ):
diff --git a/tools/annotation_profiler/scripts/build_profile_indexes.py b/tools/annotation_profiler/scripts/build_profile_indexes.py
index a4fe4c60..42a598de 100644
--- a/tools/annotation_profiler/scripts/build_profile_indexes.py
+++ b/tools/annotation_profiler/scripts/build_profile_indexes.py
@@ -257,7 +257,7 @@ def __main__():
                 chrom_lengths[ fields[0] ] = int( fields[ 1 ] )
             chroms = chrom_lengths.keys()
             print 'Chrom info taken from chromInfo.txt.gz.'
-        except Exception, e:
+        except Exception as e:
             print 'Error loading chrom info from chromInfo.txt.gz, trying FTP method.'
             chrom_lengths = {} #zero out chrom_lengths
             chroms = []
diff --git a/tools/annotation_profiler/tool_dependencies.xml b/tools/annotation_profiler/tool_dependencies.xml
deleted file mode 100644
index be8e0569..00000000
--- a/tools/annotation_profiler/tool_dependencies.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bx-python" version="0.7.1">
-    <repository name="package_bx_python_0_7" owner="devteam" />
-  </package>
-</tool_dependency>
diff --git a/tools/best_regression_subsets/best_regression_subsets.py b/tools/best_regression_subsets/best_regression_subsets.py
index 00328bb9..a3eab7db 100644
--- a/tools/best_regression_subsets/best_regression_subsets.py
+++ b/tools/best_regression_subsets/best_regression_subsets.py
@@ -42,13 +42,13 @@ def stop_err(msg):
             fields = line.split("\t")
             try:
                 yval = float(fields[y_col])
-            except Exception, ey:
+            except Exception as ey:
                 yval = r('NA')
             y_vals.append(yval)
             for k, col in enumerate(x_cols):
                 try:
                     xval = float(fields[col])
-                except Exception, ex:
+                except Exception as ex:
                     xval = r('NA')
                 x_vals[k].append(xval)
         except:
@@ -65,7 +65,7 @@ def stop_err(msg):
 set_default_mode(NO_CONVERSION)
 try:
     leaps = r.regsubsets(r("y ~ x"), data= r.na_exclude(dat))
-except RException, rex:
+except RException as rex:
     stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain no numeric values.")
 set_default_mode(BASIC_CONVERSION)
 
diff --git a/tools/best_regression_subsets/best_regression_subsets.xml b/tools/best_regression_subsets/best_regression_subsets.xml
index d854d7ba..816b5945 100644
--- a/tools/best_regression_subsets/best_regression_subsets.xml
+++ b/tools/best_regression_subsets/best_regression_subsets.xml
@@ -1,4 +1,4 @@
-<tool id="BestSubsetsRegression1" name="Perform Best-subsets Regression" version="1.0.0">
+<tool id="BestSubsetsRegression1" name="Perform Best-subsets Regression" version="1.0.1">
   <description> </description>
   <requirements>
     <requirement type="package" version="1.7.1">numpy</requirement>
diff --git a/tools/best_regression_subsets/tool_dependencies.xml b/tools/best_regression_subsets/tool_dependencies.xml
deleted file mode 100644
index 8c259db3..00000000
--- a/tools/best_regression_subsets/tool_dependencies.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="numpy" version="1.7.1">
-      <repository name="package_numpy_1_7" owner="devteam" />
-    </package>
-  <package name="rpy" version="1.0.3">
-      <repository name="package_rpy_1_0_3" owner="devteam" />
-    </package>
-</tool_dependency>
diff --git a/tools/blat_coverage_report/blat_coverage_report.py b/tools/blat_coverage_report/blat_coverage_report.py
index 682bf603..f5a19da1 100644
--- a/tools/blat_coverage_report/blat_coverage_report.py
+++ b/tools/blat_coverage_report/blat_coverage_report.py
@@ -74,7 +74,7 @@ def __main__():
                 if not diff_hash.has_key((chrom, cur_index)):
                     try:
                         diff_hash[(chrom, cur_index)] = [0,0,0,0,sub_b.upper()]    # a, t, c, g, ref. nuc.
-                    except Exception, e:
+                    except Exception as e:
                         stop_err( str( e ) )
                 if sub_a in ['a','t','c','g']:
                     diff_hash[(chrom, cur_index)][nuc_index[(sub_a)]] += 1
@@ -104,4 +104,4 @@ def __main__():
     if invalid_chars:
         print 'Skipped %d invalid characters in the alignment. ' % (invalid_chars)
         
-if __name__ == '__main__': __main__()
\ No newline at end of file
+if __name__ == '__main__': __main__()
diff --git a/tools/blat_coverage_report/blat_coverage_report.xml b/tools/blat_coverage_report/blat_coverage_report.xml
index 15b9143c..1258975a 100644
--- a/tools/blat_coverage_report/blat_coverage_report.xml
+++ b/tools/blat_coverage_report/blat_coverage_report.xml
@@ -1,4 +1,4 @@
-<tool id="generate_coverage_report" name="Polymorphism of the Reads" version="1.0.0">
+<tool id="generate_coverage_report" name="Polymorphism of the Reads" version="1.0.1">
 	<description>the percentage of reads supporting each nucleotide at each location</description>
 	<command interpreter="python">blat_coverage_report.py $input1 $output1</command>
 	<inputs>	
diff --git a/tools/canonical_correlation_analysis/cca.py b/tools/canonical_correlation_analysis/cca.py
index 539b2282..40e3b428 100644
--- a/tools/canonical_correlation_analysis/cca.py
+++ b/tools/canonical_correlation_analysis/cca.py
@@ -106,7 +106,7 @@ def stop_err(msg):
     ycolnames = ["c%d" %(el+1) for el in y_cols]
     cc = r.cca(x=x_dat, y=y_dat, xlab=xcolnames, ylab=ycolnames, xcenter=r(x_center), ycenter=r(y_center), xscale=r(x_scale), yscale=r(y_scale), standardize_scores=r(std_scores))
     ftest = r.F_test_cca(cc)
-except RException, rex:
+except RException as rex:
     stop_err("Encountered error while performing CCA on the input data: %s" %(rex))
 
 set_default_mode(BASIC_CONVERSION)
@@ -155,4 +155,4 @@ def stop_err(msg):
 #r.plot(cc)
 for i in range(ncomps):
     r.helio_plot(cc, cv = i+1, main = r.paste("Explained Variance for CV",i+1), type = "variance")
-r.dev_off()
\ No newline at end of file
+r.dev_off()
diff --git a/tools/canonical_correlation_analysis/cca.xml b/tools/canonical_correlation_analysis/cca.xml
index 38572fba..efe0638d 100644
--- a/tools/canonical_correlation_analysis/cca.xml
+++ b/tools/canonical_correlation_analysis/cca.xml
@@ -1,9 +1,9 @@
-<tool id="cca1" name="Canonical Correlation Analysis" version="1.0.0">
+<tool id="cca1" name="Canonical Correlation Analysis" version="1.0.1">
   <description> </description>
   <requirements>
     <requirement type="package" version="2.11.0">R</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
-    <requirement type="package" version="1.0">yacca</requirement>
+    <requirement type="package" version="1.0">r-yacca</requirement>
     <requirement type="package" version="1.0.3">rpy</requirement>
   </requirements>
   <command interpreter="python">
diff --git a/tools/canonical_correlation_analysis/tool_dependencies.xml b/tools/canonical_correlation_analysis/tool_dependencies.xml
deleted file mode 100644
index 20c595b6..00000000
--- a/tools/canonical_correlation_analysis/tool_dependencies.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="yacca" version="1.0">
-      <repository name="package_cran_yacca_1_0" owner="devteam" />
-    </package>
-    <package name="numpy" version="1.7.1">
-      <repository name="package_numpy_1_7" owner="devteam" />
-    </package>
-    <package name="rpy" version="1.0.3">
-      <repository name="package_rpy_1_0_3" owner="devteam" />
-    </package>
-    <package name="R" version="2.11.0">
-      <repository name="package_r_2_11_0" owner="devteam" />
-    </package>
-</tool_dependency>
diff --git a/tools/ccat/ccat_wrapper.py b/tools/ccat/ccat_wrapper.py
index f21c6f57..0caaca28 100644
--- a/tools/ccat/ccat_wrapper.py
+++ b/tools/ccat/ccat_wrapper.py
@@ -34,7 +34,7 @@ def main():
         shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file )
         shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file )
         shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file )
-    except Exception, e:
+    except Exception as e:
         return stop_err( tmp_dir, e )
     os.rmdir( tmp_dir ) #clean up empty temp working directory
 
diff --git a/tools/ccat/ccat_wrapper.xml b/tools/ccat/ccat_wrapper.xml
index bc43a9dc..9cc087ac 100644
--- a/tools/ccat/ccat_wrapper.xml
+++ b/tools/ccat/ccat_wrapper.xml
@@ -1,7 +1,6 @@
-<tool id="peakcalling_ccat" name="CCAT" version="0.0.1">
+<tool id="peakcalling_ccat" name="CCAT" version="0.0.2">
   <description>Control-based ChIP-seq Analysis Tool</description>
   <requirements>
-    <requirement type="package" version="3.0">CCAT</requirement>
     <requirement type="package" version="3.0">ccat</requirement>
   </requirements>
   <command>
diff --git a/tools/ccat/tool_dependencies.xml b/tools/ccat/tool_dependencies.xml
deleted file mode 100644
index dd32498d..00000000
--- a/tools/ccat/tool_dependencies.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="CCAT" version="3.0">
-      <repository name="package_ccat_3_0" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>
diff --git a/tools/correlation/cor.py b/tools/correlation/cor.py
index 881bd951..6aa7c4dd 100644
--- a/tools/correlation/cor.py
+++ b/tools/correlation/cor.py
@@ -71,7 +71,7 @@ def main():
         # Run correlation
         try:
             value = r.cor( array( matrix ), use="pairwise.complete.obs", method=method )
-        except Exception, exc:
+        except Exception as exc:
             out.close()
             stop_err("%s" %str( exc ))
         for row in value:
diff --git a/tools/correlation/cor.xml b/tools/correlation/cor.xml
index 5186dbaa..e7f727f7 100644
--- a/tools/correlation/cor.xml
+++ b/tools/correlation/cor.xml
@@ -1,4 +1,4 @@
-<tool id="cor2" name="Correlation" version="1.0.0">
+<tool id="cor2" name="Correlation" version="1.0.1">
   <description>for numeric columns</description>
   <requirements>
     <requirement type="package" version="1.0.3">rpy</requirement>
diff --git a/tools/correlation/tool_dependencies.xml b/tools/correlation/tool_dependencies.xml
deleted file mode 100644
index aad4f58b..00000000
--- a/tools/correlation/tool_dependencies.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="rpy" version="1.0.3">
-      <repository name="package_rpy_1_0_3" owner="devteam" />
-    </package>
-</tool_dependency>
diff --git a/tools/featurecounter/featureCounter.py b/tools/featurecounter/featureCounter.py
index 9942fd0b..9c4d378d 100644
--- a/tools/featurecounter/featureCounter.py
+++ b/tools/featurecounter/featureCounter.py
@@ -128,7 +128,7 @@ def main():
                 out_file.write( "%s\n" % "\t".join( line.fields ) )
             else:
                 out_file.write( "%s\n" % line )
-    except ParseError, exc:
+    except ParseError as exc:
         out_file.close()
         fail( str( exc ) )
 
diff --git a/tools/featurecounter/featureCounter.xml b/tools/featurecounter/featureCounter.xml
index b13a18a3..b08802e8 100644
--- a/tools/featurecounter/featureCounter.xml
+++ b/tools/featurecounter/featureCounter.xml
@@ -1,4 +1,4 @@
-<tool id="featureCoverage1" name="Feature coverage" version="2.0.0">
+<tool id="featureCoverage1" name="Feature coverage" version="2.0.1">
   <description></description>
   <requirements>
     <requirement type="package" version="0.7.1">bx-python</requirement>
diff --git a/tools/featurecounter/tool_dependencies.xml b/tools/featurecounter/tool_dependencies.xml
deleted file mode 100644
index 919796c5..00000000
--- a/tools/featurecounter/tool_dependencies.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bx-python" version="0.7.1">
-      <repository name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="galaxy-ops" version="1.0.0">
-      <repository name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>
diff --git a/tools/getindelrates_3way/getIndelRates_3way.py b/tools/getindelrates_3way/getIndelRates_3way.py
index a5877d06..5d2f109a 100755
--- a/tools/getindelrates_3way/getIndelRates_3way.py
+++ b/tools/getindelrates_3way/getIndelRates_3way.py
@@ -130,7 +130,7 @@ def main():
                 elif elems[1].endswith('delete'):
                     deletes[sp_ind] += 1
                 prev_bnum = new_bnum
-            except Exception, ei:
+            except Exception as ei:
                 #print >>sys.stderr, ei
                 continue
         irate = []
diff --git a/tools/getindelrates_3way/getIndelRates_3way.xml b/tools/getindelrates_3way/getIndelRates_3way.xml
index ce6a02b2..8bb24827 100644
--- a/tools/getindelrates_3way/getIndelRates_3way.xml
+++ b/tools/getindelrates_3way/getIndelRates_3way.xml
@@ -1,4 +1,4 @@
-<tool id="indelRates_3way" name="Estimate Indel Rates" version="1.0.0">
+<tool id="indelRates_3way" name="Estimate Indel Rates" version="1.0.1">
   <description> for 3-way alignments</description>
   <requirements>
     <requirement type="package" version="0.7.1">bx-python</requirement>
diff --git a/tools/getindelrates_3way/tool_dependencies.xml b/tools/getindelrates_3way/tool_dependencies.xml
deleted file mode 100644
index 919796c5..00000000
--- a/tools/getindelrates_3way/tool_dependencies.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bx-python" version="0.7.1">
-      <repository name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="galaxy-ops" version="1.0.0">
-      <repository name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>
diff --git a/tools/kernel_canonical_correlation_analysis/kcca.py b/tools/kernel_canonical_correlation_analysis/kcca.py
index 4f131285..fa154a65 100644
--- a/tools/kernel_canonical_correlation_analysis/kcca.py
+++ b/tools/kernel_canonical_correlation_analysis/kcca.py
@@ -122,7 +122,7 @@ def stop_err(msg):
     
 try:
     kcc = r.kcca(x=x_dat, y=y_dat, kernel=kernel, kpar=pars, ncomps=ncomps)
-except RException, rex:
+except RException as rex:
     raise
     log.exception( rex )
     stop_err("Encountered error while performing kCCA on the input data: %s" %(rex))
diff --git a/tools/kernel_canonical_correlation_analysis/kcca.xml b/tools/kernel_canonical_correlation_analysis/kcca.xml
index b1e2e8ea..8df8c7a4 100644
--- a/tools/kernel_canonical_correlation_analysis/kcca.xml
+++ b/tools/kernel_canonical_correlation_analysis/kcca.xml
@@ -1,4 +1,4 @@
-<tool id="kcca1" name="Kernel Canonical Correlation Analysis" version="1.0.0">
+<tool id="kcca1" name="Kernel Canonical Correlation Analysis" version="1.0.1">
   <description> </description>
   <requirements>
     <requirement type="package" version="1.0.3">rpy</requirement>
diff --git a/tools/kernel_principal_component_analysis/kpca.py b/tools/kernel_principal_component_analysis/kpca.py
index 833b4215..c69bda8b 100644
--- a/tools/kernel_principal_component_analysis/kpca.py
+++ b/tools/kernel_principal_component_analysis/kpca.py
@@ -101,7 +101,7 @@ def stop_err(msg):
     
 try:
     kpc = r.kpca(x=r.na_exclude(dat), kernel=kernel, kpar=pars, features=ncomps)
-except RException, rex:
+except RException as rex:
     stop_err("Encountered error while performing kPCA on the input data: %s" %(rex))
 set_default_mode(BASIC_CONVERSION)
     
@@ -131,4 +131,4 @@ def stop_err(msg):
     r.pairs(rotated,labels=r.list(range(1,ncomps+1)),main="Scatterplot of rotated values")
 else:
     r.plot(rotated, ylab='Comp.1', main="Scatterplot of rotated values")
-r.dev_off()
\ No newline at end of file
+r.dev_off()
diff --git a/tools/kernel_principal_component_analysis/kpca.xml b/tools/kernel_principal_component_analysis/kpca.xml
index ec476e09..1b266e79 100644
--- a/tools/kernel_principal_component_analysis/kpca.xml
+++ b/tools/kernel_principal_component_analysis/kpca.xml
@@ -1,9 +1,9 @@
-<tool id="kpca1" name="Kernel Principal Component Analysis" version="1.0.0">
+<tool id="kpca1" name="Kernel Principal Component Analysis" version="1.0.1">
   <description> </description>
   <requirements>
     <requirement type="package" version="1.0.3">rpy</requirement>
-    <requirement type="package" version="2.11.0">R</requirement>
-    <requirement type="package" version="0.1-4">kernlab</requirement>
+    <requirement type="package" version="2.11.0">r-base</requirement>
+    <requirement type="package" version="0.1-4">r-kernlab</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
     <requirement type="package" version="0.7.1">bx-python</requirement>
   </requirements>
diff --git a/tools/kernel_principal_component_analysis/tool_dependencies.xml b/tools/kernel_principal_component_analysis/tool_dependencies.xml
deleted file mode 100644
index 194f807e..00000000
--- a/tools/kernel_principal_component_analysis/tool_dependencies.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="rpy" version="1.0.3">
-      <repository name="package_rpy_1_0_3" owner="devteam" />
-    </package>
-    <package name="R" version="2.11.0">
-      <repository name="package_r_2_11_0" owner="devteam" />
-    </package>
-    <package name="numpy" version="1.7.1">
-      <repository name="package_numpy_1_7" owner="devteam" />
-    </package>
-    <package name="bx-python" version="0.7.1">
-      <repository name="package_bx_python_0_7" owner="devteam" />
-    </package>
-    <package name="kernlab" version="0.1-4">
-      <repository name="package_cran_kernlab_0_1_4" owner="devteam" />
-    </package>
-</tool_dependency>
diff --git a/tools/linear_regression/linear_regression.py b/tools/linear_regression/linear_regression.py
index e40b9984..f1dd3da4 100644
--- a/tools/linear_regression/linear_regression.py
+++ b/tools/linear_regression/linear_regression.py
@@ -61,7 +61,7 @@ def stop_err(msg):
 set_default_mode(NO_CONVERSION)
 try:
     linear_model = r.lm(r("y ~ x"), data = r.na_exclude(dat))
-except RException, rex:
+except RException as rex:
     stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain only non-numeric or invalid values.")
 set_default_mode(BASIC_CONVERSION)
 
diff --git a/tools/linear_regression/linear_regression.xml b/tools/linear_regression/linear_regression.xml
index 7445d88b..89927c24 100644
--- a/tools/linear_regression/linear_regression.xml
+++ b/tools/linear_regression/linear_regression.xml
@@ -1,4 +1,4 @@
-<tool id="LinearRegression1" name="Perform Linear Regression" version="1.0.1">
+<tool id="LinearRegression1" name="Perform Linear Regression" version="1.0.2">
   <description> </description>
   <requirements>
     <requirement type="package" version="2.11.0">R</requirement>
diff --git a/tools/linear_regression/tool_dependencies.xml b/tools/linear_regression/tool_dependencies.xml
deleted file mode 100644
index df11781f..00000000
--- a/tools/linear_regression/tool_dependencies.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="numpy" version="1.7.1">
-      <repository name="package_numpy_1_7" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="rpy" version="1.0.3">
-      <repository name="package_rpy_1_0_3" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="R" version="2.11.0">
-      <repository name="package_r_2_11_0" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>
diff --git a/tools/logistic_regression_vif/logistic_regression_vif.py b/tools/logistic_regression_vif/logistic_regression_vif.py
index 254d3889..4cf0f5aa 100755
--- a/tools/logistic_regression_vif/logistic_regression_vif.py
+++ b/tools/logistic_regression_vif/logistic_regression_vif.py
@@ -76,7 +76,7 @@ def stop_err(msg):
 set_default_mode(NO_CONVERSION)
 try:
     linear_model = r.glm(r("y ~ x"), data=r.na_exclude(dat), family="binomial")
-except RException, rex:
+except RException as rex:
     stop_err("Error performing logistic regression on the input data.\nEither the response column or one of the predictor columns contain only non-numeric or invalid values.")
 if len(x_cols)>1:
     try:
@@ -84,7 +84,7 @@ def stop_err(msg):
         r.assign('dat', dat)
         r.assign('ncols', len(x_cols))
         vif = r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx), family="binomial")'))
-    except RException, rex:
+    except RException as rex:
         print rex
 else:
     novif = 1
diff --git a/tools/logistic_regression_vif/logistic_regression_vif.xml b/tools/logistic_regression_vif/logistic_regression_vif.xml
index 3947add8..e724f590 100755
--- a/tools/logistic_regression_vif/logistic_regression_vif.xml
+++ b/tools/logistic_regression_vif/logistic_regression_vif.xml
@@ -1,4 +1,4 @@
-<tool id="LogisticRegression" name="Perform Logistic Regression with vif" version="1.0.1">
+<tool id="LogisticRegression" name="Perform Logistic Regression with vif" version="1.0.2">
   <description> </description>
   <requirements>
     <requirement type="package" version="1.7.1">numpy</requirement>
diff --git a/tools/logistic_regression_vif/tool_dependencies.xml b/tools/logistic_regression_vif/tool_dependencies.xml
deleted file mode 100644
index df11781f..00000000
--- a/tools/logistic_regression_vif/tool_dependencies.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="numpy" version="1.7.1">
-      <repository name="package_numpy_1_7" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="rpy" version="1.0.3">
-      <repository name="package_rpy_1_0_3" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="R" version="2.11.0">
-      <repository name="package_r_2_11_0" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>
diff --git a/tools/mapping_to_ucsc/mapping_to_ucsc.py b/tools/mapping_to_ucsc/mapping_to_ucsc.py
index 285ca505..de6cd559 100644
--- a/tools/mapping_to_ucsc/mapping_to_ucsc.py
+++ b/tools/mapping_to_ucsc/mapping_to_ucsc.py
@@ -37,7 +37,7 @@ def main():
     sorted_infile = tempfile.NamedTemporaryFile()
     try:
         os.system("sort -k %d,%d -k %dn -o %s %s" %(chr_col+1,chr_col+1,coord_col+1,sorted_infile.name,in_fname))
-    except Exception, exc:
+    except Exception as exc:
         stop_err( 'Initialization error -> %s' %str(exc) )
 
     #generate chr list
@@ -200,4 +200,4 @@ def main():
         fout.seek(0)
         os.system("cat %s %s %s %s %s | cat > %s" %(fout.name,fout_a.name,fout_t.name,fout_g.name,fout_c.name,out_fname))
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()
diff --git a/tools/mapping_to_ucsc/mapping_to_ucsc.xml b/tools/mapping_to_ucsc/mapping_to_ucsc.xml
index 75397a39..536c9e0c 100644
--- a/tools/mapping_to_ucsc/mapping_to_ucsc.xml
+++ b/tools/mapping_to_ucsc/mapping_to_ucsc.xml
@@ -1,4 +1,4 @@
-<tool id="mapToUCSC" name="Format mapping data" version="1.0.0">
+<tool id="mapToUCSC" name="Format mapping data" version="1.0.1">
   <description> as UCSC custom track</description>
   <command interpreter="python">
   	mapping_to_ucsc.py 
diff --git a/tools/megablast_wrapper/megablast_wrapper.py b/tools/megablast_wrapper/megablast_wrapper.py
index 44787910..937f29bf 100644
--- a/tools/megablast_wrapper/megablast_wrapper.py
+++ b/tools/megablast_wrapper/megablast_wrapper.py
@@ -89,7 +89,7 @@ def __main__():
             raise Exception, stderr
         if os.path.exists( tmp ):
             os.unlink( tmp )
-    except Exception, e:
+    except Exception as e:
         if os.path.exists( mega_temp_output ):
             os.unlink( mega_temp_output )
         if os.path.exists( tmp ):
diff --git a/tools/megablast_wrapper/megablast_wrapper.xml b/tools/megablast_wrapper/megablast_wrapper.xml
index 4ed09d0b..a3e9b0d1 100644
--- a/tools/megablast_wrapper/megablast_wrapper.xml
+++ b/tools/megablast_wrapper/megablast_wrapper.xml
@@ -1,7 +1,7 @@
-<tool id="megablast_wrapper" name="Megablast" version="1.2.0">
+<tool id="megablast_wrapper" name="Megablast" version="1.2.1">
     <description> compare short reads against htgs, nt, and wgs databases</description>
     <requirements>
-        <requirement type="package" version="2.2.26+">blast+</requirement>
+        <requirement type="package" version="2.10.1">blast</requirement>
         <requirement type="package" version="0.7.1">bx-python</requirement>
     </requirements>
     <command interpreter="python">
diff --git a/tools/megablast_wrapper/tool_dependencies.xml b/tools/megablast_wrapper/tool_dependencies.xml
deleted file mode 100644
index afcf65b1..00000000
--- a/tools/megablast_wrapper/tool_dependencies.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="blast+" version="2.2.26+">
-        <repository name="package_blast_plus_2_2_26" owner="devteam" />
-    </package>
-    <package name="bx-python" version="0.7.1">
-        <repository name="package_bx_python_0_7" owner="devteam" />
-    </package>
-</tool_dependency>
diff --git a/tools/microsats_mutability/microsats_mutability.py b/tools/microsats_mutability/microsats_mutability.py
index 5c4d7a7c..4895aed4 100644
--- a/tools/microsats_mutability/microsats_mutability.py
+++ b/tools/microsats_mutability/microsats_mutability.py
@@ -483,7 +483,7 @@ def main():
                     linestr += "\n"
                 prev_bnum = new_bnum
             output_writer(prev_bnum, linestr.strip().replace('\r','\n').split('\n'))
-        except Exception, ea:
+        except Exception as ea:
             print >> sys.stderr, ea
             skipped += 1
         if skipped:
diff --git a/tools/microsats_mutability/microsats_mutability.xml b/tools/microsats_mutability/microsats_mutability.xml
index 8872901c..b1d0ef63 100644
--- a/tools/microsats_mutability/microsats_mutability.xml
+++ b/tools/microsats_mutability/microsats_mutability.xml
@@ -1,4 +1,4 @@
-<tool id="microsats_mutability1" name="Estimate microsatellite mutability" version="1.1.0">
+<tool id="microsats_mutability1" name="Estimate microsatellite mutability" version="1.1.1">
   <description>by specified attributes</description>
   <requirements>
     <requirement type="package" version="0.7.1">bx-python</requirement>
diff --git a/tools/microsats_mutability/tool_dependencies.xml b/tools/microsats_mutability/tool_dependencies.xml
deleted file mode 100644
index 919796c5..00000000
--- a/tools/microsats_mutability/tool_dependencies.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bx-python" version="0.7.1">
-      <repository name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="galaxy-ops" version="1.0.0">
-      <repository name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>
diff --git a/tools/partialr_square/partialR_square.py b/tools/partialr_square/partialR_square.py
index 3d97248b..b66a8da3 100755
--- a/tools/partialr_square/partialR_square.py
+++ b/tools/partialr_square/partialR_square.py
@@ -62,14 +62,14 @@ def sscombs(s):
             fields = line.split("\t")
             try:
                 yval = float(fields[y_col])
-            except Exception, ey:
+            except Exception as ey:
                 yval = r('NA')
                 #print >> sys.stderr, "ey = %s" %ey
             y_vals.append(yval)
             for k, col in enumerate(x_cols):
                 try:
                     xval = float(fields[col])
-                except Exception, ex:
+                except Exception as ex:
                     xval = r('NA')
                     #print >> sys.stderr, "ex = %s" %ex
                 x_vals[k].append(xval)
@@ -82,7 +82,7 @@ def sscombs(s):
 set_default_mode(NO_CONVERSION)
 try:
     full = r.lm(r("y ~ x"), data= r.na_exclude(dat))    #full model includes all the predictor variables specified by the user
-except RException, rex:
+except RException as rex:
     stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain no numeric values.")
 set_default_mode(BASIC_CONVERSION)
 
diff --git a/tools/partialr_square/partialR_square.xml b/tools/partialr_square/partialR_square.xml
index 08eb50ac..2c0ab32b 100755
--- a/tools/partialr_square/partialR_square.xml
+++ b/tools/partialr_square/partialR_square.xml
@@ -1,4 +1,4 @@
-<tool id="partialRsq" name="Compute partial R square" version="1.0.0">
+<tool id="partialRsq" name="Compute partial R square" version="1.0.1">
   <description> </description>
   <requirements>
     <requirement type="package" version="2.11.0">R</requirement>
diff --git a/tools/partialr_square/tool_dependencies.xml b/tools/partialr_square/tool_dependencies.xml
deleted file mode 100644
index df11781f..00000000
--- a/tools/partialr_square/tool_dependencies.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="numpy" version="1.7.1">
-      <repository name="package_numpy_1_7" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="rpy" version="1.0.3">
-      <repository name="package_rpy_1_0_3" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="R" version="2.11.0">
-      <repository name="package_r_2_11_0" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>
diff --git a/tools/pileup_interval/pileup_interval.py b/tools/pileup_interval/pileup_interval.py
index 455b8cad..3597db11 100644
--- a/tools/pileup_interval/pileup_interval.py
+++ b/tools/pileup_interval/pileup_interval.py
@@ -59,12 +59,12 @@ def __main__():
         lineParts = inLine.split('\t')
         try:
             seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex])
-        except IndexError, ei:
+        except IndexError as ei:
             if options.format == 'ten':
                 stop_err( 'It appears that you have selected 10 columns while your file has 6. Make sure that the number of columns you specify matches the number in your file.\n' + str( ei ) )
             else:
                 stop_err( 'There appears to be something wrong with your column index values.\n' + str( ei ) )
-        except ValueError, ev:
+        except ValueError as ev:
             if options.format == 'six':
                 stop_err( 'It appears that you have selected 6 columns while your file has 10. Make sure that the number of columns you specify matches the number in your file.\n' + str( ev ) )
             else:
diff --git a/tools/pileup_interval/pileup_interval.xml b/tools/pileup_interval/pileup_interval.xml
index da4288b6..463dc503 100644
--- a/tools/pileup_interval/pileup_interval.xml
+++ b/tools/pileup_interval/pileup_interval.xml
@@ -1,4 +1,4 @@
-<tool id="pileup_interval" name="Pileup-to-Interval" version="1.0.2">
+<tool id="pileup_interval" name="Pileup-to-Interval" version="1.0.3">
   <description>condenses pileup format into ranges of bases</description>
   <command interpreter="python">
     pileup_interval.py 
diff --git a/tools/principal_component_analysis/pca.py b/tools/principal_component_analysis/pca.py
index 79242416..f25970c2 100644
--- a/tools/principal_component_analysis/pca.py
+++ b/tools/principal_component_analysis/pca.py
@@ -74,7 +74,7 @@ def stop_err(msg):
         pc = r.princomp(r.na_exclude(dat), cor = r("FALSE"))
     elif method=="svd":
         pc = r.prcomp(r.na_exclude(dat), center = r(center), scale = r(scale))
-except RException, rex:
+except RException as rex:
     stop_err("Encountered error while performing PCA on the input data: %s" %(rex))
 
 set_default_mode(BASIC_CONVERSION)
@@ -126,4 +126,4 @@ def stop_err(msg):
 
 r.pdf( outfile2, 8, 8 )
 r.biplot(pc)
-r.dev_off()
\ No newline at end of file
+r.dev_off()
diff --git a/tools/principal_component_analysis/pca.xml b/tools/principal_component_analysis/pca.xml
index ad7ed537..cf1438b3 100644
--- a/tools/principal_component_analysis/pca.xml
+++ b/tools/principal_component_analysis/pca.xml
@@ -1,4 +1,4 @@
-<tool id="pca1" name="Principal Component Analysis" version="1.0.2">
+<tool id="pca1" name="Principal Component Analysis" version="1.0.3">
   <description> </description>
   <requirements>
     <requirement type="package" version="1.0.3">rpy</requirement>
diff --git a/tools/principal_component_analysis/tool_dependencies.xml b/tools/principal_component_analysis/tool_dependencies.xml
deleted file mode 100644
index d8da26ff..00000000
--- a/tools/principal_component_analysis/tool_dependencies.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="numpy" version="1.7.1">
-      <repository name="package_numpy_1_7" owner="devteam" />
-    </package>
-    <package name="rpy" version="1.0.3">
-      <repository name="package_rpy_1_0_3" owner="devteam" />
-    </package>
-    <package name="R" version="2.11.0">
-      <repository name="package_r_2_11_0" owner="devteam" />
-    </package>
-</tool_dependency>
diff --git a/tools/quality_filter/quality_filter.py b/tools/quality_filter/quality_filter.py
index af2b70c4..13aae8e2 100644
--- a/tools/quality_filter/quality_filter.py
+++ b/tools/quality_filter/quality_filter.py
@@ -120,7 +120,7 @@ def main():
                         continue
             except:
                 pass
-    except Exception, exc:
+    except Exception as exc:
         stop_err( 'Initialization errorL %s' % str( exc ) )
     
     if len(pspecies) == 0:
@@ -136,7 +136,7 @@ def main():
     try:
         maf_reader = bx.align.maf.Reader( open(inp_file, 'r') )
         maf_writer = bx.align.maf.Writer( open(out_file,'w') )
-    except Exception, e:
+    except Exception as e:
         stop_err( "Your MAF file appears to be malformed: %s" % str( e ) )
     
     maf_count = 0
@@ -214,7 +214,7 @@ def main():
         for stat in status_strings[1:]:
             try:
                 output_status_str = bitwise_and (status_strings[0], stat, '0')
-            except Exception, e:
+            except Exception as e:
                 break
             
         for seq in range (len(block.components)):
diff --git a/tools/quality_filter/quality_filter.xml b/tools/quality_filter/quality_filter.xml
index 6c4820b5..1a15fe22 100644
--- a/tools/quality_filter/quality_filter.xml
+++ b/tools/quality_filter/quality_filter.xml
@@ -1,4 +1,4 @@
-<tool id="qualityFilter" name="Filter nucleotides" version="1.0.1">
+<tool id="qualityFilter" name="Filter nucleotides" version="1.0.2">
   <description> based on quality scores</description>
   <requirements>
     <requirement type="package" version="0.7.1">bx-python</requirement>
diff --git a/tools/quality_filter/tool_dependencies.xml b/tools/quality_filter/tool_dependencies.xml
deleted file mode 100644
index 55c8b5ec..00000000
--- a/tools/quality_filter/tool_dependencies.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bx-python" version="0.7.1">
-      <repository name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="numpy" version="1.7.1">
-      <repository name="package_numpy_1_7" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>
diff --git a/tools/rcve/rcve.py b/tools/rcve/rcve.py
index 48a8d48a..bdb531f0 100644
--- a/tools/rcve/rcve.py
+++ b/tools/rcve/rcve.py
@@ -59,14 +59,14 @@ def sscombs(s):
             fields = line.split("\t")
             try:
                 yval = float(fields[y_col])
-            except Exception, ey:
+            except Exception as ey:
                 yval = r('NA')
                 #print >>sys.stderr, "ey = %s" %ey
             y_vals.append(yval)
             for k, col in enumerate(x_cols):
                 try:
                     xval = float(fields[col])
-                except Exception, ex:
+                except Exception as ex:
                     xval = r('NA')
                     #print >>sys.stderr, "ex = %s" %ex
                 x_vals[k].append(xval)
@@ -79,7 +79,7 @@ def sscombs(s):
 set_default_mode(NO_CONVERSION)
 try:
     full = r.lm( r("y ~ x"), data=r.na_exclude(dat) )  #full model includes all the predictor variables specified by the user
-except RException, rex:
+except RException as rex:
     stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain no numeric values.")
 set_default_mode(BASIC_CONVERSION)
 
diff --git a/tools/rcve/rcve.xml b/tools/rcve/rcve.xml
index d430d1f6..6bfee8e2 100644
--- a/tools/rcve/rcve.xml
+++ b/tools/rcve/rcve.xml
@@ -1,4 +1,4 @@
-<tool id="rcve1" name="Compute RCVE" version="1.0.0">
+<tool id="rcve1" name="Compute RCVE" version="1.0.1">
   <description> </description>
   <requirements>
     <requirement type="package" version="2.11.0">R</requirement>
diff --git a/tools/rcve/tool_dependencies.xml b/tools/rcve/tool_dependencies.xml
deleted file mode 100644
index df11781f..00000000
--- a/tools/rcve/tool_dependencies.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="numpy" version="1.7.1">
-      <repository name="package_numpy_1_7" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="rpy" version="1.0.3">
-      <repository name="package_rpy_1_0_3" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="R" version="2.11.0">
-      <repository name="package_r_2_11_0" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>
diff --git a/tools/rmap/rmap_wrapper.py b/tools/rmap/rmap_wrapper.py
index c061bebc..66b492e8 100644
--- a/tools/rmap/rmap_wrapper.py
+++ b/tools/rmap/rmap_wrapper.py
@@ -71,12 +71,12 @@ def __main__():
         #print command
         try:
             os.system( command )
-        except Exception, e:
+        except Exception as e:
             stop_err( str( e ) )
 
         try:
             os.system( 'cat %s >> %s' % ( output_tempfile, output_file ) )
-        except Exception, e:
+        except Exception as e:
             stop_err( str( e ) )
         
         try:
diff --git a/tools/rmap/rmap_wrapper.xml b/tools/rmap/rmap_wrapper.xml
index 24f074b0..8b8e50fd 100644
--- a/tools/rmap/rmap_wrapper.xml
+++ b/tools/rmap/rmap_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="rmap_wrapper" name="RMAP" version="1.0.0">
+<tool id="rmap_wrapper" name="RMAP" version="1.0.1">
     <description>for Solexa Short Reads Alignment</description>
     <requirements>
       <requirement type="package" version="2.05">rmap</requirement>
diff --git a/tools/rmap/tool_dependencies.xml b/tools/rmap/tool_dependencies.xml
deleted file mode 100644
index 5f7ca565..00000000
--- a/tools/rmap/tool_dependencies.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="rmap" version="2.05">
-    <repository name="package_rmap_2_05" owner="devteam" />
-  </package>
-</tool_dependency>
diff --git a/tools/rmapq/rmapq_wrapper.py b/tools/rmapq/rmapq_wrapper.py
index 84957872..84bdbcb9 100644
--- a/tools/rmapq/rmapq_wrapper.py
+++ b/tools/rmapq/rmapq_wrapper.py
@@ -83,12 +83,12 @@ def __main__():
         #print command
         try:
             os.system( command )
-        except Exception, e:
+        except Exception as e:
             stop_err( str( e ) )
 
         try:
             assert os.system( 'cat %s >> %s' % ( output_tempfile, output_file ) ) == 0
-        except Exception, e:
+        except Exception as e:
             stop_err( str( e ) )
         
         try:
diff --git a/tools/rmapq/rmapq_wrapper.xml b/tools/rmapq/rmapq_wrapper.xml
index 6a37a74d..c43fd531 100644
--- a/tools/rmapq/rmapq_wrapper.xml
+++ b/tools/rmapq/rmapq_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="rmapq_wrapper" name="RMAPQ" version="1.0.0">
+<tool id="rmapq_wrapper" name="RMAPQ" version="1.0.1">
     <description>for Solexa Short Reads Alignment with Quality Scores</description>
     <requirements>
       <requirement type="package" version="2.05">rmap</requirement>
diff --git a/tools/rmapq/tool_dependencies.xml b/tools/rmapq/tool_dependencies.xml
deleted file mode 100644
index 5f7ca565..00000000
--- a/tools/rmapq/tool_dependencies.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="rmap" version="2.05">
-    <repository name="package_rmap_2_05" owner="devteam" />
-  </package>
-</tool_dependency>
diff --git a/tools/tophat/tool_dependencies.xml b/tools/tophat/tool_dependencies.xml
deleted file mode 100644
index aa8eedac..00000000
--- a/tools/tophat/tool_dependencies.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bowtie" version="0.12.7">
-      <repository name="package_bowtie_0_12_7" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="samtools" version="0.1.18">
-      <repository name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" />
-    </package>
-    <package name="tophat" version="1.4.0">
-      <repository name="package_tophat_1_4_0" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>
diff --git a/tools/tophat/tophat_wrapper.py b/tools/tophat/tophat_wrapper.py
index 8492be6f..f8d6c828 100644
--- a/tools/tophat/tophat_wrapper.py
+++ b/tools/tophat/tophat_wrapper.py
@@ -123,7 +123,7 @@ def __main__():
             tmp_stderr.close()
             if returncode != 0:
                 raise Exception, stderr
-        except Exception, e:
+        except Exception as e:
             if os.path.exists( tmp_index_dir ):
                 shutil.rmtree( tmp_index_dir )
             stop_err( 'Error indexing reference sequence\n' + str( e ) )
@@ -194,7 +194,7 @@ def __main__():
             if options.max_segment_intron:
                 opts += ' --max-segment-intron %d' % int( options.max_segment_intron )
             cmd = cmd % ( opts, index_path, reads )
-        except Exception, e:
+        except Exception as e:
             # Clean up temp dirs
             if os.path.exists( tmp_index_dir ):
                 shutil.rmtree( tmp_index_dir )
@@ -228,7 +228,7 @@ def __main__():
             raise Exception, stderr
             
         # TODO: look for errors in program output.
-    except Exception, e:
+    except Exception as e:
         stop_err( 'Error in tophat:\n' + str( e ) ) 
 
     # Clean up temp dirs
diff --git a/tools/tophat/tophat_wrapper.xml b/tools/tophat/tophat_wrapper.xml
index 48aaa260..605ca536 100644
--- a/tools/tophat/tophat_wrapper.xml
+++ b/tools/tophat/tophat_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="tophat" name="TopHat for Illumina" version="1.5.0">
+<tool id="tophat" name="TopHat for Illumina" version="1.5.1">
     <!-- Wrapper compatible with TopHat versions 1.3.0 to 1.4.1 -->
     <description>Find splice junctions using RNA-seq data</description>
     <version_command>tophat --version</version_command>
diff --git a/tools/weightedaverage/WeightedAverage.py b/tools/weightedaverage/WeightedAverage.py
index 0a29d65f..f6506e83 100755
--- a/tools/weightedaverage/WeightedAverage.py
+++ b/tools/weightedaverage/WeightedAverage.py
@@ -55,7 +55,7 @@ def get_float_no_zero( field ):
     chr_col_1, start_col_1, end_col_1, strand_col1 = parse_cols_arg( options.cols1 )
     chr_col_2, start_col_2, end_col_2, strand_col2, name_col_2 = parse_cols_arg( options.cols2 )
     input1, input2, input3 = args
-except Exception, eee:
+except Exception as eee:
     print eee
     stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
 
diff --git a/tools/weightedaverage/WeightedAverage.xml b/tools/weightedaverage/WeightedAverage.xml
index 326e27eb..e725d6b8 100755
--- a/tools/weightedaverage/WeightedAverage.xml
+++ b/tools/weightedaverage/WeightedAverage.xml
@@ -1,4 +1,4 @@
-<tool id="wtavg" name="Assign weighted-average" version="1.0.1">
+<tool id="wtavg" name="Assign weighted-average" version="1.0.2">
   <description> of the values of features overlapping an interval </description>
   <requirements>
     <requirement type="package" version="1.0.0">galaxy-ops</requirement>
@@ -79,4 +79,4 @@ The output will contain all the columns in the first input plus a new column con
 
 
 </help>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/weightedaverage/tool_dependencies.xml b/tools/weightedaverage/tool_dependencies.xml
deleted file mode 100644
index bc83a66f..00000000
--- a/tools/weightedaverage/tool_dependencies.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bx-python" version="0.7.1">
-      <repository name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" />
-    </package>
-  <package name="galaxy-ops" version="1.0.0">
-      <repository name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" />
-    </package>
-</tool_dependency>