diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index b1ae11265c3..4eec287995a 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -17,11 +17,11 @@
     <tool file="data_source/encode_import_gencode.xml" />
   </section>
   <section name="ENCODE Tools" id="EncodeTools">
-    <tool file="encode/gencode_partition.xml" />
-    <tool file="encode/random_intervals.xml" />
+    <tool file="encode/gencode_partition1/1.0.0/gencode_partition.xml" />
+    <tool file="encode/random_intervals1/1.0.0/random_intervals.xml" />
   </section>
   <section name="Lift-Over" id="liftOver">
-    <tool file="extract/liftOver_wrapper.xml" />
+    <tool file="extract/liftOver1/1.0.0/liftOver_wrapper.xml" />
   </section>
   <section name="Text Manipulation" id="textutil">
     <tool file="filters/fixedValueColumn.xml" />
@@ -57,7 +57,7 @@
   </section>
   <section name="Extract Features" id="features">
     <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
-    <tool file="extract/extract_GFF_Features.xml" />
+    <tool file="extract/Extract_features1/1.0.0/extract_GFF_Features.xml" />
   </section>
   <!--  
   <section name="Pattern-Matching" id="patmat">
@@ -67,10 +67,10 @@
   <section name="Fetch Sequences" id="fetchSeq">
     <!-- 
     These are deprecated
-    <tool file="extract/fasta-subseq-wrapper.xml" />
-    <tool file="extract/twoBitToFa_wrapper.xml" />
+    <tool file="extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper.xml" />
+    <tool file="extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa_wrapper.xml" />
     -->
-    <tool file="extract/extract_genomic_dna.xml" />
+    <tool file="extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna.xml" />
   </section>
   <section name="Fetch Alignments" id="fetchAlign">
     <tool file="maf/interval2maf_pairwise.xml" />
@@ -90,7 +90,7 @@
   <section name="Get Genomic Scores" id="scores">
     <tool file="stats/wiggle_to_simple.xml" />
     <tool file="stats/aggregate_binned_scores_in_intervals.xml" />
-    <tool file="extract/phastOdds/phastOdds_tool.xml" />
+    <tool file="extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml" />
   </section>
   <section name="Operate on Genomic Intervals" id="bxops">
   	<tool file="new_operations/intersect.xml" id="intersect" />  
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 11ef91c6465..f8f73eaa6a2 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -21,11 +21,11 @@
     <tool file="data_source/encode_import_gencode.xml" />
   </section>
   <section name="ENCODE Tools" id="EncodeTools">
-    <tool file="encode/gencode_partition.xml" />
-    <tool file="encode/random_intervals.xml" />
+    <tool file="encode/gencode_partition1/1.0.0/gencode_partition.xml" />
+    <tool file="encode/random_intervals1/1.0.0/random_intervals.xml" />
   </section>
   <section name="Lift-Over" id="liftOver">
-    <tool file="extract/liftOver_wrapper.xml" />
+    <tool file="extract/liftOver1/1.0.0/liftOver_wrapper.xml" />
   </section>
   <section name="Text Manipulation" id="textutil">
     <tool file="filters/fixedValueColumn.xml" />
@@ -65,7 +65,7 @@
   </section>
   <section name="Extract Features" id="features">
     <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
-    <tool file="extract/extract_GFF_Features.xml" />
+    <tool file="extract/Extract_features1/1.0.0/extract_GFF_Features.xml" />
   </section>
   <section name="Pattern-Matching" id="patmat">
     <tool file="patmat/findcluster_mysql.xml" />
@@ -73,10 +73,10 @@
   <section name="Fetch Sequences" id="fetchSeq">
     <!-- 
     These are deprecated
-    <tool file="extract/fasta-subseq-wrapper.xml" />
-    <tool file="extract/twoBitToFa_wrapper.xml" />
+    <tool file="extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper.xml" />
+    <tool file="extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa_wrapper.xml" />
     -->
-    <tool file="extract/extract_genomic_dna.xml" />
+    <tool file="extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna.xml" />
   </section>
   <section name="Fetch Alignments" id="fetchAlign">
     <tool file="maf/interval2maf_pairwise.xml" />
@@ -94,7 +94,7 @@
   <section name="Get Genomic Scores" id="scores">
     <tool file="stats/wiggle_to_simple.xml" />
     <tool file="stats/aggregate_binned_scores_in_intervals.xml" />
-    <tool file="extract/phastOdds/phastOdds_tool.xml" />
+    <tool file="extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml" />
   </section>
   <section name="Operate on Genomic Intervals" id="bxops">
   	<tool file="new_operations/intersect.xml" id="intersect" />  
diff --git a/tools/encode/gencode_partition.xml b/tools/encode/gencode_partition1/1.0.0/gencode_partition.xml
similarity index 100%
rename from tools/encode/gencode_partition.xml
rename to tools/encode/gencode_partition1/1.0.0/gencode_partition.xml
diff --git a/tools/encode/split_by_partitions.py b/tools/encode/gencode_partition1/1.0.0/split_by_partitions.py
similarity index 100%
rename from tools/encode/split_by_partitions.py
rename to tools/encode/gencode_partition1/1.0.0/split_by_partitions.py
diff --git a/tools/encode/random_intervals.xml b/tools/encode/random_intervals1/1.0.0/random_intervals.xml
similarity index 86%
rename from tools/encode/random_intervals.xml
rename to tools/encode/random_intervals1/1.0.0/random_intervals.xml
index 215545a588e..36420158774 100644
--- a/tools/encode/random_intervals.xml
+++ b/tools/encode/random_intervals1/1.0.0/random_intervals.xml
@@ -21,6 +21,13 @@
         <filter type="column" name="value_col" value="1" />
       </options>
     </param> 
+    <!--
+    <param name="regions" type="select" label="Regions to use">
+      <options from_file="/depot/data2/galaxy/phastOdds.loc" name_col="2" value_col="1">
+        <filter type="data_meta" data_ref="input" meta_key="dbkey" meta_key_col="0" />
+      </options>
+    </param> 
+    -->
   </inputs>
   <outputs>
     <data name="out_file1" format="input"/>
diff --git a/tools/encode/random_intervals_no_bits.py b/tools/encode/random_intervals1/1.0.0/random_intervals_no_bits.py
similarity index 100%
rename from tools/encode/random_intervals_no_bits.py
rename to tools/encode/random_intervals1/1.0.0/random_intervals_no_bits.py
diff --git a/tools/extract/extractAxt_wrapper.pl b/tools/extract/Extract_blastz_alignments1/1.0.0/extractAxt_wrapper.pl
similarity index 100%
rename from tools/extract/extractAxt_wrapper.pl
rename to tools/extract/Extract_blastz_alignments1/1.0.0/extractAxt_wrapper.pl
diff --git a/tools/extract/extractAxt_wrapper.xml b/tools/extract/Extract_blastz_alignments1/1.0.0/extractAxt_wrapper.xml
similarity index 100%
rename from tools/extract/extractAxt_wrapper.xml
rename to tools/extract/Extract_blastz_alignments1/1.0.0/extractAxt_wrapper.xml
diff --git a/tools/extract/extract_GFF_Features.py b/tools/extract/Extract_features1/1.0.0/extract_GFF_Features.py
similarity index 100%
rename from tools/extract/extract_GFF_Features.py
rename to tools/extract/Extract_features1/1.0.0/extract_GFF_Features.py
diff --git a/tools/extract/extract_GFF_Features.xml b/tools/extract/Extract_features1/1.0.0/extract_GFF_Features.xml
similarity index 100%
rename from tools/extract/extract_GFF_Features.xml
rename to tools/extract/Extract_features1/1.0.0/extract_GFF_Features.xml
diff --git a/tools/extract/fasta-subseq-wrapper.pl b/tools/extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper.pl
similarity index 100%
rename from tools/extract/fasta-subseq-wrapper.pl
rename to tools/extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper.pl
diff --git a/tools/extract/fasta-subseq-wrapper.xml b/tools/extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper.xml
similarity index 100%
rename from tools/extract/fasta-subseq-wrapper.xml
rename to tools/extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper.xml
diff --git a/tools/extract/fasta-subseq-wrapper_code.py b/tools/extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper_code.py
similarity index 100%
rename from tools/extract/fasta-subseq-wrapper_code.py
rename to tools/extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper_code.py
diff --git a/tools/extract/twoBitToFa b/tools/extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa
similarity index 100%
rename from tools/extract/twoBitToFa
rename to tools/extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa
diff --git a/tools/extract/twoBitToFa_wrapper.py b/tools/extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa_wrapper.py
similarity index 100%
rename from tools/extract/twoBitToFa_wrapper.py
rename to tools/extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa_wrapper.py
diff --git a/tools/extract/twoBitToFa_wrapper.xml b/tools/extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa_wrapper.xml
similarity index 100%
rename from tools/extract/twoBitToFa_wrapper.xml
rename to tools/extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa_wrapper.xml
diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna.py
similarity index 100%
rename from tools/extract/extract_genomic_dna.py
rename to tools/extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna.py
diff --git a/tools/extract/extract_genomic_dna.xml b/tools/extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna.xml
similarity index 100%
rename from tools/extract/extract_genomic_dna.xml
rename to tools/extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna.xml
diff --git a/tools/extract/extract_genomic_dna_code.py b/tools/extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna_code.py
similarity index 100%
rename from tools/extract/extract_genomic_dna_code.py
rename to tools/extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna_code.py
diff --git a/tools/extract/liftOver_wrapper.py b/tools/extract/liftOver1/1.0.0/liftOver_wrapper.py
similarity index 100%
rename from tools/extract/liftOver_wrapper.py
rename to tools/extract/liftOver1/1.0.0/liftOver_wrapper.py
diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver1/1.0.0/liftOver_wrapper.xml
similarity index 100%
rename from tools/extract/liftOver_wrapper.xml
rename to tools/extract/liftOver1/1.0.0/liftOver_wrapper.xml
diff --git a/tools/extract/liftOver_wrapper_code.py b/tools/extract/liftOver1/1.0.0/liftOver_wrapper_code.py
similarity index 100%
rename from tools/extract/liftOver_wrapper_code.py
rename to tools/extract/liftOver1/1.0.0/liftOver_wrapper_code.py
diff --git a/tools/extract/phastOdds/get_scores_galaxy.py b/tools/extract/phastOdds/phastOdds_for_intervals/1.0.0/get_scores_galaxy.py
similarity index 100%
rename from tools/extract/phastOdds/get_scores_galaxy.py
rename to tools/extract/phastOdds/phastOdds_for_intervals/1.0.0/get_scores_galaxy.py
diff --git a/tools/extract/phastOdds/phastOdds_tool.xml b/tools/extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml
similarity index 100%
rename from tools/extract/phastOdds/phastOdds_tool.xml
rename to tools/extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml