--- a/tool_dependencies.xml	Mon Jan 07 14:49:50 2013 -0600
+++ b/tool_dependencies.xml	Mon Jan 07 14:52:26 2013 -0600
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="defuse" version="0.5.0">
+    <package name="defuse" version="0.6.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.5/defuse-0.5.0.tar.gz</action>
+                <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.0.tar.gz</action>
                 <action type="shell_command">cd tools &amp;&amp; make</action>
                 <action type="move_directory_files">
                     <source_directory>.</source_directory>
@@ -15,9 +15,36 @@
             </actions>
         </install>
         <readme>
+deFuse code
+To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
         </readme>
     </package>
 
+    <package name="samtools" version="0.1.18">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
+                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>samtools</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>misc/maq2sam-long</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Compiling SAMtools requires the ncurses and zlib development libraries.
+        </readme>
+    </package>
+
+
     <package name="bowtie" version="0.12.7">
         <install version="1.0">
             <actions>
@@ -45,6 +72,65 @@
         </readme>
     </package>
 
+    <package name="gmap" version="2012-07-20">
+        <install version="1.0">
+            <actions>
+	        <action type="download_by_url" target_filename="gmap-2012-07-20.tar.gz">http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-07-20.v2.tar.gz</action>
+                <action type="shell_command">./configure</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>src/gmap</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>src/gmapindex</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>src/gsnap</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>src/uniqscan</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>src/iit_store</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>src/iit_get</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>src/atoiindex</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>src/snpindex</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>src/cmetindex</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>src/get-genome</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>util</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+
     <package name="blat" version="34x10">
         <install version="1.0">
             <actions>