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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/bgruening/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 - v0.3.1: added parallelism and changed the output parameters from boolean to a select box
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63
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64 Licence (MIT)
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65 =============
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66
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67 Permission is hereby granted, free of charge, to any person obtaining a copy
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68 of this software and associated documentation files (the "Software"), to deal
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69 in the Software without restriction, including without limitation the rights
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70 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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71 copies of the Software, and to permit persons to whom the Software is
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72 furnished to do so, subject to the following conditions:
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73
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74 The above copyright notice and this permission notice shall be included in
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75 all copies or substantial portions of the Software.
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76
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77 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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78 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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79 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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80 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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81 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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82 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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83 THE SOFTWARE.
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84
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