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1 Galaxy wrapper for t-RNA prediction tools
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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 prepository contains wrapper for the command line tools of tRNAscan-SE_ and Arogorn_.
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7
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8 .. _tRNAscan-SE: http://lowelab.ucsc.edu/tRNAscan-SE/
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9 .. _Arogorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
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10
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11 Dean Laslett and Bjorn Canback
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12 ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16
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13 doi:10.1093/nar/gkh152
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14
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15 Todd M. Lowe and Sean R. Eddy
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16 tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964
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17 doi:10.1093/nar/25.5.0955
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18
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19
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20 ============
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21 Installation
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22 ============
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23
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24 The t-RNA prediction wrappers are available through the toolshed_ and can be automatically installed.
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25
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26 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/trna_prediction
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27
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28 For manuel installation, please download tRNAscan-SE from the following URL and follow the install instructions::
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29
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30 http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz
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31
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32 Arogorn can be download from::
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33
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34 http://mbio-serv2.mbioekol.lu.se/ARAGORN/aragorn1.2.33.c
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35
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36 With a recent GNU-Compiler (gcc) you can compile it with the following command::
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37
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38 gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.33.c
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39
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40 Please include aragorn and tRNAscan-SE into your PATH::
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41
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42 export PATH=$PATH:/home/user/bin/aragorn/bin/
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43
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44
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45 To install the wrappers copy the files aragorn.xml and tRNAscan.xml in the galaxy tools
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46 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
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47 For example add the following lines::
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48
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49 <tool file="trna_prediction/aragorn.xml" />
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50 <tool file="trna_prediction/tRNAscan.xml" />
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51
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52
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53 =======
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54 History
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55 =======
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56
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57 tRNAscan:
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58
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59 - v0.1: Initial public release
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60 - v0.2: add fasta output
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61 - v0.2.1: added tool-dependency
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62 - v0.2.2: patch from Nicola Soranzo added
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63 - v0.3: add unit tests, documentation improvements, bug fixes
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64
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65 aragorn:
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66
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67 - v0.1: Initial public release
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68 - v0.2: added options, upgrade to 1.2.36, tool-dependency
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69 - v0.3: add unit tests, documentation improvements
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70
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71
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72
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73 Wrapper Licence (MIT/BSD style)
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74 ===============================
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75
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76 Permission to use, copy, modify, and distribute this software and its
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77 documentation with or without modifications and for any purpose and
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78 without fee is hereby granted, provided that any copyright notices
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79 appear in all copies and that both those copyright notices and this
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80 permission notice appear in supporting documentation, and that the
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81 names of the contributors or copyright holders not be used in
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82 advertising or publicity pertaining to distribution of the software
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83 without specific prior permission.
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84
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85 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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86 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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87 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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88 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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89 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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90 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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91 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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92 OR PERFORMANCE OF THIS SOFTWARE.
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93
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