Changes

Note that UMAKE requires external software packages to be copied to <code>$(UMAKE_HOME)/ext/</code> directory  

Note that UMAKE requires external software packages to be copied to <code>$(UMAKE_HOME)/ext/</code> directory  

* create a "ext" folder under UMAKE_HOME

* Create an "ext" folder under UMAKE_HOME

* <code>bgzip</code> and <code>tabix</code> - To download, go to [http://sourceforge.net/projects/samtools/files/tabix/ TABIX Download]

* <code>bgzip</code> and <code>tabix</code> - To download, go to [http://sourceforge.net/projects/samtools/files/tabix/ TABIX Download]

* <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]

* Copy bgzip and tabix 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 <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/

== Basic Usage Example ==

== Basic Usage Example ==