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3
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4 ===========
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5 OPPL-GALAXY
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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 oppl_galaxy_tool.jar and oppl_galaxy_tool_lib/ 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/OPPL/.
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19
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20 4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/.
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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="Ontology Pre Processor Language" id="oppl">
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25 <tool file="OPPL/oppl.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 Note that if you want you can use any java parameter by editing oppl.xml
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31 , eg: <command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000
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32 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL
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33 > $output </command>
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34
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35
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36
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37 USAGE
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38 =====
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39
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40 An ontology and an OPPL file are needed (test.owl and test.oppl can be
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41 used as samples). Load both:
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42
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43 Get Data
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44 >> Upload File from your computer
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45
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46 Then execute the OPPL file against the OWL file:
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47
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48 Ontology Pre Processor Language
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49 >> Execute an OPPL file against an OWL file
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50
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51
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52
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53 TESTS
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54 =====
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55
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56 To run the functional test, first complete installation and then:
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57
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58 1.- Copy test.owl and test.oppl to /galaxy-dist/test-data/
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59
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60 2.- Add the following lines to /galaxy-dist/tool_conf.xml.sample
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61
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62 <section name="Ontology Pre Processor Language" id="oppl">
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63 <tool file="OPPL/oppl.xml"/>
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64 </section>
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65
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66 3.- Execute /galaxy-dist/run_functional_tests.sh -id oppl
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67
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68
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69
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70 CONTACT
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71 =======
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72
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73 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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74
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75
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76
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77 ACKNOWLEDGEMENTS
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78 ================
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79
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80 This work is funded by the Marie Curie Cofund program of the EU, FP7.
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81
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82
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83
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84 COPYRIGHT AND LICENSE
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85 =====================
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86
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87 Copyright (c) 2011 Mikel Egaña Aranguren.
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88
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89 OPPL-Galaxy is free software: you can redistribute it and/or modify
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90 it under the terms of the GNU General Public License as published by
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91 the Free Software Foundation, either version 3 of the License, or
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92 (at your option) any later version.
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93
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94 This program is distributed in the hope that it will be useful,
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95 but WITHOUT ANY WARRANTY; without even the implied warranty of
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96 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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97 GNU General Public License for more details.
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98
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99 You should have received a copy of the GNU General Public License
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100 along with this program. If not, see <http://www.gnu.org/licenses/>.
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101
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102 OPPL, OWL API and Pellet have their own licenses.
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103
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104 Galaxy is distributed as open source under the conditions of the
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105 Academic Free License (http://www.opensource.org/licenses/academic.php).
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106
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107
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108
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109
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110
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111
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112
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113
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