changeset 0:b05b788e3989

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jun 06 08:25:46 2013 -0400
@@ -0,0 +1,34 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="kent" version="latest">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url" target_filename="kent.zip">http://hgdownload.cse.ucsc.edu/admin/jksrc.zip</action>
+                <action type="shell_command">
+                    export MACHTYPE=`uname -m`; 
+                    export BINDIR=$INSTALL_DIR/bin; mkdir $INSTALL_DIR/bin; 
+                    cd src/lib; make; 
+                    cd ../jkOwnLib; make; 
+                    cd ../blat; make;
+                    cd ../gfClient; make;
+                    cd ../gfServer; make;
+                    cd ../utils; mv makefile makefile.orig; grep -v -E 'pslLiftSubrangeBlat|raSqlQuery|scaffoldFaToAgp' makefile.orig > makefile;  make
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Downloads and installs the latest kent tools from UCSC at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
+( The website doesn't offer previously released versions.)
+
+NOTE: This only handles blat for a NON-COMMERCIAL system.
+
+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>