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1
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2
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3
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4 =============
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5 NCBO Services
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6 =============
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7
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8
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9
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10 INSTALLATION
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11 ============
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12
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13 1.- Stop Galaxy.
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14
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15 2.- Copy the .jar files and _lib/ directories to
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16 /galaxy-dist/tool-data/shared/jars/
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17
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18 3.- Create directory /galaxy-dist/tools/NCBO_services/
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19
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20 4.- Copy get_ontology.xml to /galaxy-dist/tools/NCBO_services/
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21
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22 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
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23
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24 <section name="NCBO services" id="NCBO_services">
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25 <tool file="NCBO_services/get_ontology.xml"/>
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26 </section>
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27
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28 6.- Start Galaxy.
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29
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30
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31
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32 USAGE
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33 =====
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34
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35 A bioportal API key and an ontology id must be provided. The API key can be
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36 obtained by creating an account at bioportal
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37 (http://bioportal.bioontology.org/). The id can be obtained in the ontology page
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38 (e.g. 1522 for BioPAX, see http://bioportal.bioontology.org/ontologies/1522)
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39
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40
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41
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42 CONTACT
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43 =======
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44
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45 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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46
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47
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48
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49 ACKNOWLEDGEMENTS
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50 ================
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51
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52 This work is funded by the Marie Curie Cofund program of the EU, FP7.
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53
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54
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55
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56 COPYRIGHT AND LICENSE
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57 =====================
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58
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59 Copyright (c) 2011 Mikel Egaña Aranguren.
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60
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61 NCBO Services is free software: you can redistribute it and/or modify
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62 it under the terms of the GNU General Public License as published by
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63 the Free Software Foundation, either version 3 of the License, or
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64 (at your option) any later version.
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65
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66 This program is distributed in the hope that it will be useful,
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67 but WITHOUT ANY WARRANTY; without even the implied warranty of
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68 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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69 GNU General Public License for more details.
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70
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71 You should have received a copy of the GNU General Public License
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72 along with this program. If not, see <http://www.gnu.org/licenses/>.
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73
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74
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75
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76
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77
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78
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79
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80
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81
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