annotate OPPL/README @ 9:14bfd77f8520

Interface improved (Imports first) and proper handling of import/merge options added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Tue, 18 Oct 2011 10:30:16 +0200
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4 ===========
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5 OPPL-GALAXY
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6 ===========
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10 INSTALLATION
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11 ============
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13 1.- Stop galaxy.
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15 2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/
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16 and oppl_galaxy_tool_lib/ to /galaxy-dist/tool-data/shared/jars/
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18 3.- Create directory /galaxy-dist/tools/OPPL/
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20 4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/
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22 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
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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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28 6.- Start galaxy.
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32 USAGE
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33 =====
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35 An ontology and an OPPL file are needed (test.owl and test.oppl can be
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36 used as samples). Load both:
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38 Get Data
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39 >> Upload File from your computer
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41 Then execute the OPPL file against the OWL file:
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43 Ontology Pre Processor Language
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44 >> Execute an OPPL file against an OWL file
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46 An ontology produced by another galaxy tools can also be used.
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48 Test.oppl and test.owl can be used as examples. More OPPL-Galaxy
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49 examples can be obtained at http://miuras.inf.um.es/OPPL-Galaxy/, and
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50 general OPPL script that may be useful to use with OPPL-Galaxy can be
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51 obtained at http://oppl2.sourceforge.net/taggedexamples/.
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55 FORESEEN FEATURES
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56 =================
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58 Choose which inferred axioms to add to the output ontology (Right now
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59 only subsumption between named classes is available).
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61 OWLLink support.
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65 KNOWN BUGS AND ISSUES
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66 =====================
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68 Currently Galaxy interprets any information thrown to stderr as a tool
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69 error, which is bad since OPPL (And many other tools) throw info to
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70 sdterr even if working properly. In OPPL Galaxy, stderr is redirected to
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71 /dev/null to avoid the problem, but that means that OPPL Galaxy does not
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72 fail gracefully (It simply stops). A wrapper will be implemented.
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74 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
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78 TESTS
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79 =====
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81 To run the functional test, first complete installation and then:
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83 1.- Copy test.owl and test.oppl to /galaxy-dist/test-data/
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84
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85 2.- Add the following lines to /galaxy-dist/tool_conf.xml.sample
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86
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87 <section name="Ontology Pre Processor Language" id="oppl">
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88 <tool file="OPPL/oppl.xml"/>
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89 </section>
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91 3.- Execute /galaxy-dist/run_functional_tests.sh -id oppl
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95 CONTACT
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96 =======
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98 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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102 ACKNOWLEDGEMENTS
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103 ================
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104
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105 This work is funded by the Marie Curie Cofund program of the EU, FP7.
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109 COPYRIGHT AND LICENSE
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110 =====================
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111
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112 Copyright (c) 2011 Mikel EgaƱa Aranguren.
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114 OPPL-Galaxy is free software: you can redistribute it and/or modify
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115 it under the terms of the GNU General Public License as published by
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116 the Free Software Foundation, either version 3 of the License, or
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117 (at your option) any later version.
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118
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119 This program is distributed in the hope that it will be useful,
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120 but WITHOUT ANY WARRANTY; without even the implied warranty of
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121 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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122 GNU General Public License for more details.
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123
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124 You should have received a copy of the GNU General Public License
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125 along with this program. If not, see <http://www.gnu.org/licenses/>.
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127 OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses.
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