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1 Galaxy wrapper for Augustus
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2 ===========================
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3
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4 This wrapper is copyright 2012-2013 by Björn Grüning.
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5
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6 This is a wrapper for the command line tool of Augustus_.
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7
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8 .. _augustus: http://bioinf.uni-greifswald.de/augustus/
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9
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10 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
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11
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12 Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
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13 A novel hybrid gene prediction method employing protein multiple sequence alignments
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14 Bioinformatics, doi: 10.1093/bioinformatics/btr010
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15
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16 Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
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17 Using native and syntenically mapped cDNA alignments to improve de novo gene finding
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18 Bioinformatics, doi: 10.1093/bioinformatics/btn013
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19
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20 Mario Stanke and Stephan Waack (2003)
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21 Gene Prediction with a Hidden-Markov Model and a new Intron Submodel.
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22 Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
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23
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24
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25 Installation
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26 ============
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27
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28 The recommended installation is by means of the toolshed_.
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29 If you need to install it manually here is a short introduction.
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30
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31 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/augustus
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32
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33
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34 Install or downlaod augustus from::
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35
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36 http://bioinf.uni-greifswald.de/augustus/binaries/
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37
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38 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.
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39
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40 For example::
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41
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42 <section name="Gene Prediction" id="gene_prediction">
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43 <tool file="gene_prediction/tools/augustus/augustus.xml" />
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44 </section>
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45
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46
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47 Set the *AUGUSTUS_CONFIG_PATH* to /path_to_augustus/augustus/config with::
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48
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49 export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
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50
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51 or modify the wrapper and use the following additional commandline switch::
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52
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53 --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
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54
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55
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56 History
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57 =======
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58
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59 - v0.1: Initial public release
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60 - v0.2: Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
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61 - v0.3: upgrade to augustus 2.7, added new organisms and new parameters, output additional sequence files
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62
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63 Wrapper Licence (MIT/BSD style)
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64 ===============================
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65
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66 Permission to use, copy, modify, and distribute this software and its
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67 documentation with or without modifications and for any purpose and
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68 without fee is hereby granted, provided that any copyright notices
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69 appear in all copies and that both those copyright notices and this
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70 permission notice appear in supporting documentation, and that the
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71 names of the contributors or copyright holders not be used in
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72 advertising or publicity pertaining to distribution of the software
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73 without specific prior permission.
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74
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75 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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76 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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77 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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78 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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79 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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80 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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81 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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82 OR PERFORMANCE OF THIS SOFTWARE.
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83
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