diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index bb1ffc04602..5fe6ade6020 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -113,8 +113,8 @@
     <tool file="plotting/histogram_rpy/1.0.0/histogram2.xml" />
     <tool file="plotting/scatterplot_rpy/1.0.0/scatterplot.xml" />
     <tool file="plotting/XY_Plot_1/1.0.0/xy_plot.xml" />
-    <tool file="visualization/GMAJ.xml" />
-    <tool file="visualization/build_ucsc_custom_track.xml" />
+    <tool file="visualization/gmaj_1/1.0.0/GMAJ.xml" />
+    <tool file="visualization/build_ucsc_custom_track_1/1.0.0/build_ucsc_custom_track.xml" />
   </section>
   <section name="Regional Variation" id="regVar">
   	<tool file="regVariation/winSplitter/1.0.0/windowSplitter.xml" />
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 9d100d33d3e..eb28080f817 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -10,7 +10,7 @@
     <tool file="data_source/biomart_test.xml" />
     <tool file="data_source/encode_db.xml" />
     <tool file="data_source/hbvar.xml" /> 
-    <tool file="validation/fix_errors.xml" />
+    <tool file="validation/fix_errors/1.0.0/fix_errors.xml" />
   </section>
   <section name="Get ENCODE Data" id="encode">
     <tool file="data_source/encode_import_chromatin_and_chromosomes.xml"/>
@@ -117,9 +117,9 @@
     <tool file="plotting/histogram_rpy/1.0.0/histogram2.xml" />
     <tool file="plotting/scatterplot_rpy/1.0.0/scatterplot.xml" />
     <tool file="plotting/XY_Plot_1/1.0.0/xy_plot.xml" />
-    <tool file="visualization/GMAJ.xml" />
-    <tool file="visualization/LAJ.xml" />
-    <tool file="visualization/build_ucsc_custom_track.xml" />
+    <tool file="visualization/gmaj_1/1.0.0/GMAJ.xml" />
+    <tool file="visualization/laj_1/1.0.0/LAJ.xml" />
+    <tool file="visualization/build_ucsc_custom_track_1/1.0.0/build_ucsc_custom_track.xml" />
   </section>
   <section name="Regional Variation" id="regVar">
   	<tool file="regVariation/winSplitter/1.0.0/windowSplitter.xml" />
diff --git a/tools/validation/fix_errors.py b/tools/validation/fix_errors/1.0.0/fix_errors.py
similarity index 100%
rename from tools/validation/fix_errors.py
rename to tools/validation/fix_errors/1.0.0/fix_errors.py
diff --git a/tools/validation/fix_errors.xml b/tools/validation/fix_errors/1.0.0/fix_errors.xml
similarity index 100%
rename from tools/validation/fix_errors.xml
rename to tools/validation/fix_errors/1.0.0/fix_errors.xml
diff --git a/tools/validation/fix_errors_code.py b/tools/validation/fix_errors/1.0.0/fix_errors_code.py
similarity index 100%
rename from tools/validation/fix_errors_code.py
rename to tools/validation/fix_errors/1.0.0/fix_errors_code.py
diff --git a/tools/validation/validate.py b/tools/validation/fix_errors/1.0.0/validate.py
similarity index 100%
rename from tools/validation/validate.py
rename to tools/validation/fix_errors/1.0.0/validate.py
diff --git a/tools/visualization/build_ucsc_custom_track.py b/tools/visualization/build_ucsc_custom_track_1/1.0.0/build_ucsc_custom_track.py
similarity index 100%
rename from tools/visualization/build_ucsc_custom_track.py
rename to tools/visualization/build_ucsc_custom_track_1/1.0.0/build_ucsc_custom_track.py
diff --git a/tools/visualization/build_ucsc_custom_track.xml b/tools/visualization/build_ucsc_custom_track_1/1.0.0/build_ucsc_custom_track.xml
similarity index 100%
rename from tools/visualization/build_ucsc_custom_track.xml
rename to tools/visualization/build_ucsc_custom_track_1/1.0.0/build_ucsc_custom_track.xml
diff --git a/tools/visualization/build_ucsc_custom_track_code.py b/tools/visualization/build_ucsc_custom_track_1/1.0.0/build_ucsc_custom_track_code.py
similarity index 100%
rename from tools/visualization/build_ucsc_custom_track_code.py
rename to tools/visualization/build_ucsc_custom_track_1/1.0.0/build_ucsc_custom_track_code.py
diff --git a/tools/visualization/GMAJ.py b/tools/visualization/gmaj_1/1.0.0/GMAJ.py
similarity index 100%
rename from tools/visualization/GMAJ.py
rename to tools/visualization/gmaj_1/1.0.0/GMAJ.py
diff --git a/tools/visualization/GMAJ.xml b/tools/visualization/gmaj_1/1.0.0/GMAJ.xml
similarity index 100%
rename from tools/visualization/GMAJ.xml
rename to tools/visualization/gmaj_1/1.0.0/GMAJ.xml
diff --git a/tools/visualization/LAJ.py b/tools/visualization/laj_1/1.0.0/LAJ.py
similarity index 100%
rename from tools/visualization/LAJ.py
rename to tools/visualization/laj_1/1.0.0/LAJ.py
diff --git a/tools/visualization/LAJ.xml b/tools/visualization/laj_1/1.0.0/LAJ.xml
similarity index 100%
rename from tools/visualization/LAJ.xml
rename to tools/visualization/laj_1/1.0.0/LAJ.xml
diff --git a/tools/visualization/LAJ_code.py b/tools/visualization/laj_1/1.0.0/LAJ_code.py
similarity index 100%
rename from tools/visualization/LAJ_code.py
rename to tools/visualization/laj_1/1.0.0/LAJ_code.py