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TASSEL 3.0 / 4.0 Pipeline Command Line Interface: Guide to using Tassel Pipeline
Terry Casstevens (tmc46@cornell.edu)
Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853-2703
October 31, 2013
Prerequisites ............................................................................................................................................................ 1!
Source Code ............................................................................................................................................................ 1!
Install ....................................................................................................................................................................... 1!
Execute .................................................................................................................................................................... 1!
Increasing Heap Size ............................................................................................................................................... 2!
Examples ................................................................................................................................................................. 2!
Examples (XML Configuration Files) .................................................................................................................... 2!
Usage ....................................................................................................................................................................... 3!
Pipeline Controls ................................................................................................................................................. 3!
Data ..................................................................................................................................................................... 3!
Analysis............................................................................................................................................................... 8!
Results ............................................................................................................................................................... 10!
Prerequisites
• Java SDK 6.0 or later (http://java.sun.com/javase/downloads/index.jsp).
• Tassel Standalone Build (http://www.maizegenetics.net/tassel/tassel3.0_standalone.zip)
• Tassel Standalone Build (http://www.maizegenetics.net/tassel/tassel4.0_standalone.zip)
Source Code
• https://tassel.svn.sourceforge.net/svnroot/tassel/maizegenetics
Install
Unzip the Tassel Standalone Build onto your file system. Change into the root directory:
tassel3.0_standalone or tassel4.0_standalone.
Execute
On Windows, use run_pipeline.bat to execute the pipeline.
In UNIX, use run_pipeline.pl to execute the pipeline. If you are using a Bash Shell on Windows, you
may need to change the following line to use a ; instead of a :.
my $CP = join(":", @fl);
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