diff --git a/scripts/migrate_tools/0008_tools.xml b/scripts/migrate_tools/0008_tools.xml
index dca874a3149..f48ba655fc6 100644
--- a/scripts/migrate_tools/0008_tools.xml
+++ b/scripts/migrate_tools/0008_tools.xml
@@ -15,16 +15,16 @@
     <repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes">
         <tool id="ctdBatch_1" version="1.0.0" file="ctd.xml" />
     </repository>
-    <repository owner="devteam" changeset_revision="9d35cf35634e" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool.">
+    <repository owner="devteam" changeset_revision="9a3f7a890da6" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool.">
         <tool id="cuffcompare" version="0.0.5" file="cuffcompare_wrapper.xml" />
     </repository>
     <repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool.">
         <tool id="cuffdiff" version="0.0.6" file="cuffdiff_wrapper.xml" />
     </repository>
-    <repository owner="devteam" changeset_revision="b50aacc8ae49" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool.">
+    <repository owner="devteam" changeset_revision="b01956f26c36" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool.">
         <tool id="cufflinks" version="0.0.6" file="cufflinks_wrapper.xml" />
     </repository>
-    <repository owner="devteam" changeset_revision="dbbd37e013aa" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool.">
+    <repository owner="devteam" changeset_revision="fdc55fd74f78" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool.">
         <tool id="cuffmerge" version="0.0.5" file="cuffmerge_wrapper.xml" />
     </repository>
     <repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file">
diff --git a/tool-data/sam_fa_indices.loc.sample b/tool-data/sam_fa_indices.loc.sample
deleted file mode 100644
index d06993b359d..00000000000
--- a/tool-data/sam_fa_indices.loc.sample
+++ /dev/null
@@ -1,28 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a sam_fa_indices.loc file 
-#similar to this one (store it in this directory) that points to 
-#the directories in which those files are stored. The sam_fa_indices.loc 
-#file has this format (white space characters are TAB characters):
-#
-#index	<seq>	<location>
-#
-#So, for example, if you had hg18 indexed stored in 
-#/depot/data2/galaxy/sam/, 
-#then the sam_fa_indices.loc entry would look like this:
-#
-#index	hg18	/depot/data2/galaxy/sam/hg18.fa
-#
-#and your /depot/data2/galaxy/sam/ directory
-#would contain hg18.fa and hg18.fa.fai files:
-#
-#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
-#
-#Your sam_fa_indices.loc file should include an entry per line for 
-#each index set you have stored.  The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file.  For example:
-#
-#index	hg18	/depot/data2/galaxy/sam/hg18.fa
-#index	hg19	/depot/data2/galaxy/sam/hg19.fa
diff --git a/tool_data_table_conf.xml.sample b/tool_data_table_conf.xml.sample
index 5ea328f1bc6..c5adcfeb2b7 100644
--- a/tool_data_table_conf.xml.sample
+++ b/tool_data_table_conf.xml.sample
@@ -55,11 +55,6 @@
         <columns>value, name, path</columns>
         <file path="tool-data/perm_color_index.loc" />
     </table>
-    <!-- Location of SAMTools indexes and other files -->
-    <table name="sam_fa_indexes" comment_char="#">
-        <columns>line_type, value, path</columns>
-        <file path="tool-data/sam_fa_indices.loc" />
-    </table>
     <!-- Location of Picard dict file and other files -->
     <table name="picard_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>