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+Galaxy wrapper for Augustus
+===========================
+
+This wrapper is copyright 2012-2013 by Björn Grüning.
+
+This is a wrapper for the command line tool of Augustus_.
+
+.. _augustus: http://bioinf.uni-greifswald.de/augustus/
+
+AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
+
+Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
+A novel hybrid gene prediction method employing protein multiple sequence alignments
+Bioinformatics, doi: 10.1093/bioinformatics/btr010
+
+Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
+Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+Bioinformatics, doi: 10.1093/bioinformatics/btn013
+
+Mario Stanke and Stephan Waack (2003)
+Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. 
+Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
+
+
+Installation
+============
+
+The recommended installation is by means of the toolshed_.
+If you need to install it manually here is a short introduction.
+
+.. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/augustus
+
+
+Install or downlaod augustus from::
+
+    http://bioinf.uni-greifswald.de/augustus/binaries/
+
+and follow the installation instructions or copy the binaries into your $PATH. To install the wrapper copy the augustus folder in the galaxy tools folder and modify the tools_conf.xml file to make the tool available to Galaxy.
+
+For example::
+
+  <section name="Gene Prediction" id="gene_prediction">
+    <tool file="gene_prediction/tools/augustus/augustus.xml" />
+  </section>
+
+
+Set the *AUGUSTUS_CONFIG_PATH* to /path_to_augustus/augustus/config with::
+
+  export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+
+or modify the wrapper and use the following additional commandline switch::
+
+  --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+
+
+History
+=======
+
+- v0.1: Initial public release
+- v0.2: Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
+- v0.3: upgrade to augustus 2.7, added new organisms and new parameters, output additional sequence files
+
+Wrapper Licence (MIT/BSD style)
+===============================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
+