annotate readme.txt @ 2:d5d5999ff4f1

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author Bjoern Gruening <bjoern@gruenings.eu>
date Thu, 15 Mar 2012 10:09:28 +0100
parents augustus/readme.txt@9fb7ae02453c
children 02e9daf33c24
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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 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 http://bioinf.uni-greifswald.de/augustus/
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8
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9 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
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10
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11 Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
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12 A novel hybrid gene prediction method employing protein multiple sequence alignments
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13 Bioinformatics, doi: 10.1093/bioinformatics/btr010
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14
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15 Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
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16 Using native and syntenically mapped cDNA alignments to improve de novo gene finding
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17 Bioinformatics, doi: 10.1093/bioinformatics/btn013
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18
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19 Mario Stanke and Stephan Waack (2003)
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20 Gene Prediction with a Hidden-Markov Model and a new Intron Submodel.
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21 Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
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22
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24
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25
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26 Installation
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27 ============
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28
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29 Install or downlaod augustus from:
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30
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31 http://bioinf.uni-greifswald.de/augustus/binaries/
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32
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33 and follow the installation instructions or copy the binaries into your $PATH
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34
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35 To install the wrapper copy the augustus folder in the galaxy tools
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36 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
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37 For example:
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38
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39 <section name="Gene Prediction" id="gene_prediction">
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40 <tool file="gene_prediction/tools/augustus/augustus.xml" />
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41 </section>
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42
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43
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44 Set the AUGUSTUS_CONFIG_PATH to /path_to_augustus/augustus/config with
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45 export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
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46 or modify the wrapper and use the following additional commandline switch:
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47 --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
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48
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50
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51
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52 History
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53 =======
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54
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55 v0.1 - Initial public release
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56
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57
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58 Wrapper Licence (MIT/BSD style)
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59 ===============================
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60
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61 Permission to use, copy, modify, and distribute this software and its
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62 documentation with or without modifications and for any purpose and
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63 without fee is hereby granted, provided that any copyright notices
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64 appear in all copies and that both those copyright notices and this
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65 permission notice appear in supporting documentation, and that the
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66 names of the contributors or copyright holders not be used in
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67 advertising or publicity pertaining to distribution of the software
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68 without specific prior permission.
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69
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70 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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71 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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72 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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73 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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74 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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75 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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76 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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77 OR PERFORMANCE OF THIS SOFTWARE.
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