--- a/tool_dependencies.xml	Wed Aug 14 04:02:28 2013 -0400
+++ b/tool_dependencies.xml	Wed Jan 29 16:12:38 2014 -0500
@@ -2,15 +2,16 @@
     <package name="blat" version="35x1">
         <install version="1.0">
             <actions>
+
                 <action type="download_binary">
-                    <url_template os="linux" architecture="x86_64">https://github.com/bgruening/download_store/raw/master/ucsc/linux/x86_64/blat_35x1</url_template>
-                    <url_template os="darwin" architecture="i686">https://github.com/bgruening/download_store/raw/master/ucsc/darwin/i386/blat_35x1</url_template>
-                    <url_template os="darwin" architecture="i386">https://github.com/bgruening/download_store/raw/master/ucsc/darwin/i386/blat_35x1</url_template>
-                    <url_template os="darwin" architecture="x86_64">https://github.com/bgruening/download_store/raw/master/ucsc/darwin/x86_64/blat_35x1</url_template>
+                    <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>
                 </action>
 
                 <action type="move_file">
-                    <source>$INSTALL_DIR/blat_35x1</source>
+                    <source>$INSTALL_DIR/blat</source>
                     <destination>$INSTALL_DIR/blat</destination>
                 </action>
                 <action type="chmod">
@@ -20,14 +21,25 @@
                     <environment_variable name="PATH" action="append_to">$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>
         <readme>
-        blat programm from the UCSC. http://genome.ucsc.edu/FAQ/FAQblat.html
+BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html
+Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git
 
-        Please note that the Blat source and executables are freely available for
-        academic, nonprofit and personal use. Commercial licensing information is
-        available on the Kent Informatics website (http://www.kentinformatics.com/).
+Please note that the BLAT source and executables are freely available for
+academic, nonprofit and personal use. Commercial licensing information is
+available on the Kent Informatics website (http://www.kentinformatics.com/).
         </readme>
     </package>
 </tool_dependency>