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1 Galaxy wrapper for AntiSmash
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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 antiSMASH.
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7
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8 antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
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9 It integrates and cross-links with a large number of in silico secondary metabolite analysis tools.
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10
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11 http://antismash.secondarymetabolites.org/
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12
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13 Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling & Eriko Takano (2011).
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14 antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research 39: W339-W346.
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15
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16
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17 Installation
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18 ============
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19
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20 Currently these wrapper is tested with version 1.1 and the modified version of antismash.py included in that repository.
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21
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22 Install or downlaod antiSMASH from:
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23
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24
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25 https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2
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26
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27
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28 ... and follow the instructions.
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29 Please replace the antismash.py file with the one inlcuded in that repository.
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30 Edit the following lines in multi_antiSMASH_wrapper.py and antiSMASH_wrapper.py and adopt it to your installation.
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31
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32 blastdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
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33 pfamdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
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34 antismash_path = '/home/galaxy/bin/antismash-1.1.0/antismash.py'
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35
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36
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37 To install the wrapper copy the antiSMASH folder in the galaxy tools
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38 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
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39 For example:
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40
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41 <section name="PKS-NRPS prediction" id="pks-nrps_prediction">
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42 <tool file="pks-nrps/tools/antiSMASH/antiSMASH.xml" />
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43 <tool file="pks-nrps/tools/antiSMASH/multi_antiSMASH.xml" />
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44 </section>
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45
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46
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4
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47 external Data
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48 =============
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49
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50 The antismash.loc file contains the path to a PFAM database.
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51 For any other tool that also uses a PFAM database *.log file, you can sync or link both *.loc files.
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52
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53
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54
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55 History
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56 =======
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57
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58 v0.1 - Initial public release
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59
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60
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61 Wrapper Licence (MIT/BSD style)
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62 ===============================
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63
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64 Permission to use, copy, modify, and distribute this software and its
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65 documentation with or without modifications and for any purpose and
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66 without fee is hereby granted, provided that any copyright notices
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67 appear in all copies and that both those copyright notices and this
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68 permission notice appear in supporting documentation, and that the
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69 names of the contributors or copyright holders not be used in
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70 advertising or publicity pertaining to distribution of the software
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71 without specific prior permission.
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72
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73 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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74 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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75 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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76 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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77 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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78 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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79 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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80 OR PERFORMANCE OF THIS SOFTWARE.
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81
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