Changes

(after compiling the source code, copy bgzip and tabix to the "ext" folder above)

(after compiling the source code, copy bgzip and tabix to the "ext" folder above)

* <code>beagle</code> - To download, go to [http://faculty.washington.edu/browning/beagle/beagle.html#download BEAGLE Download]

* <code>beagle</code> - To download, go to [http://faculty.washington.edu/browning/beagle/beagle.html#download BEAGLE Download] (Rename "beagle.jar" to "beagle.20101226.jar" and copy it to the "ext" folder)

* Copy the executables <code>bgzip</code> and <code>tabix</code> to /usr/cluster/bin/ or replace "/usr/cluster/bin" with the complete path of the above "ext" folder at line 652 and 654 of umake.pl under $(UMAKE_HOME)/scripts/

* Copy the executables <code>bgzip</code> and <code>tabix</code> to /usr/cluster/bin/ OR you could replace "/usr/cluster/bin" with the complete path of the above "ext" folder at line 652 and 654 of umake.pl under $(UMAKE_HOME)/scripts/

== Basic Usage Example ==

== Basic Usage Example ==