--- a/tool_dependencies.xml	Wed Jan 29 16:12:38 2014 -0500
+++ b/tool_dependencies.xml	Thu Jan 30 08:29:22 2014 -0500
@@ -2,34 +2,18 @@
     <package name="blat" version="35x1">
         <install version="1.0">
             <actions>
-
-                <action type="download_binary">
-                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</url_template>
-                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/blat/blat</url_template>
-                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/blat/blat</url_template>
-                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat/blat</url_template>
+                <!-- finally go back to the original version and compile blat and the entire server from source 
+                    Thanks to Nicola Soranzo.
+                    The problem is that the binaries are not versioned and we can't guarantee reproducibility. 
+                    The source packages are versioned and are stored for a long time.
+                -->
+                <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action>
+                <action type="shell_command">export HOME=$INSTALL_DIR &amp;&amp; mkdir -p $HOME/bin/$MACHTYPE &amp;&amp; make MACHTYPE=`uname -m` &amp;&amp; mv $HOME/bin/$MACHTYPE/* $HOME/bin/</action>
+                <action type="set_environment">
+                  <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>
+                  <environment_variable name="BLAT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>
 
-                <action type="move_file">
-                    <source>$INSTALL_DIR/blat</source>
-                    <destination>$INSTALL_DIR/blat</destination>
-                </action>
-                <action type="chmod">
-                    <file mode="755">$INSTALL_DIR/blat</file>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="append_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="BLAT_PATH" action="append_to">$INSTALL_DIR</environment_variable>
-                </action>
-
-                <!--
-                Alternative version from Nicola Soranzo.
-                <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action>
-                <action type="shell_command">export MACHTYPE=`uname -m` &amp;&amp; export HOME=$INSTALL_DIR &amp;&amp; mkdir -p $HOME/bin/$MACHTYPE &amp;&amp; make</action>
-                <action type="set_environment">
-                  <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/`uname -m`</environment_variable>
-                </action>
-                -->
 
             </actions>
         </install>