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+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/iuc/gatk2
+
+Galaxy should be able to 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 information:
+
+http://www.broadinstitute.org/gatk/download
+
+Once you have installed GATK2, you need to edit the env.sh files that are installed together with the wrappers.
+You must edit the GATK2_PATH environment variable in the file:
+
+<tool_dependency_dir>/environment_settings/GATK2_PATH/iuc/gatk2/<hash_string>/env.sh
+
+to point to the folder where you have installed GATK2.
+
+Optionally, you may also want to edit the GATK2_SITE_OPTIONS environment variable in the file:
+
+<tool_dependency_dir>/environment_settings/GATK2_SITE_OPTIONS/iuc/gatk2/<hash_string>/env.sh
+
+to deactivate the 'call home feature' of GATK with something like:
+
+GATK2_SITE_OPTIONS='-et NO_ET -K /data/gatk2_key_file'
+
+GATK2_SITE_OPTIONS can be also used to insert other specific options into every GATK2 wrapper
+at runtime, without changing the actual wrapper.
+
+Read more about the "Phone Home" problem at:
+http://www.broadinstitute.org/gatk/guide/article?id=1250
+
+Optionally, you may also want to add some commands to be executed before GATK (e.g. to load modules) to the file:
+::
+    <tool_dependency_dir>/gatk2/default/env.sh
+
+Note that due to the manual nature of the GATK2 installation you will be getting the 
+following warnings in the Galaxy log (unless you specified the env.sh in the previous paragraph):
+::
+    Failed to resolve dependency on 'gatk2', ignoring.
+
+This is because the 
+::
+    <requirement type="package">gatk2</requirement>
+is specified but never resolved in the tool_dependencies.xml. It is safe to ignore.
+
+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 in the tool-data/ Galaxy directory.
+
+History
+=======
+
+* v0.1      - Initial public release
+* v2.8.0    - Bugfix release, increase version number to reflect the underlying GATK version
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.