Galaxy wrapper for GATK2
========================

This wrapper is copyright 2013 by Björn Grüning, Jim Johnson & the Galaxy Team.

The Genome Analysis Toolkit or GATK is a software package developed at the 
Broad Institute to analyse next-generation resequencing data. The toolkit offers
a wide variety of tools, with a primary focus on variant discovery and 
genotyping as well as strong emphasis on data quality assurance. Its robust 
architecture, powerful processing engine and high-performance computing features
make it capable of taking on projects of any size.

http://www.broadinstitute.org/gatk
http://www.broadinstitute.org/gatk/about/citing-gatk


GATK is Free for academics, and fee for commercial use. Please study the GATK licensing website:
http://www.broadinstitute.org/gatk/about/#licensing


Installation
============

The recommended installation is by means of the toolshed_.

.. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/augustus

Galaxy should be able to automatically install samtools dependencies automatically
for you. GATK2, and its new licence model, does not allow us to distribute the GATK binaries.
As a consequence you need to install GATK2 by your own, please see the GATK website for more informations:

http://www.broadinstitute.org/gatk/download

Once you have installed GATK2 you need to edit the env.sh file that is installed with these wrappers.
You will find this env.sh file under:

<tool_dependency_dir>/gatk2/<version>/iuc/<hash_string>/env.sh

You should edit the GATK2_PATH environment variable to point to the folder you have installed GATK2
and if you want to deactivate the 'call home feature' from GATK you can set

GATK2_SITE_OPTIONS='-et "NO_ET" -K "/data/gatk2_key_file"'

GATK2_SITE_OPTIONS can be used to insert specific options into every GATK2 wrapper 
during runtime, without changing the actuall wrapper.

Read more about the "Phone Home" problem under:
http://www.broadinstitute.org/gatk/guide/article?id=1250


Finally, you should fill in additional information about your genomes and 
annotations in the gatk2_picard_index.loc and gatk2_annotations.txt. 
You can find them under ./tool-data/.



History
=======

v0.1 - Initial public release


Licence (MIT)
=============

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of this software and associated documentation files (the "Software"), to deal
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The above copyright notice and this permission notice shall be included in
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