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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 2012-2014 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 Galaxy should be able to automatically install the dependencies, i.e. the
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21 'package_hmmer_3_0' or 'package_blast_plus_2_2_28' repository.
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22
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23 You must tell Galaxy about any system level Pfam databases using the configuration
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24 file antismash.loc.
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25
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26 You can download the Pfam provided databases as compressed archives from here:
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27
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28 * ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/
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29
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30
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31 External Data
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32 =============
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33
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34 The antismash.loc file contains the path to a Pfam database.
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35 For any other tool that also uses a Pfam database *.log file, you can sync or link both *.loc files.
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36
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37
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38
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39 History
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40 =======
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41
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42 v0.1 - Initial public release
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43
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44
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45 Licence (MIT)
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46 =============
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47
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48 Permission is hereby granted, free of charge, to any person obtaining a copy
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49 of this software and associated documentation files (the "Software"), to deal
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50 in the Software without restriction, including without limitation the rights
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51 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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52 copies of the Software, and to permit persons to whom the Software is
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53 furnished to do so, subject to the following conditions:
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54
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55 The above copyright notice and this permission notice shall be included in
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56 all copies or substantial portions of the Software.
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57
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58 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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59 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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60 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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61 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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62 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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63 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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64 THE SOFTWARE.
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65
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