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annotate OPPL/README @ 15:622cde484f4c draft

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Add new tool to perform OPPL queries
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Thu, 12 Jul 2012 17:12:00 +0200
parents 7e6604a5ee55
children c9e01f86b07c
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4 INSTALLATION
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5 ============
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7 1.- Stop Galaxy.
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9 2.- Copy the following files and dirs to
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10 /galaxy-dist/tool-data/shared/jars/:
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12 oppl_galaxy_tool.jar
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13 inference.jar
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14 query.jar
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15 oppl_query.jar
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16 oppl_galaxy_lib/
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17 inference_lib/
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18 query_lib/
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19 oppl_query_lib/
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20 FaCT++-linux-v1.5.2/
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21 FaCT++-OSX-v1.5.2/
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23 3.- Create directory /galaxy-dist/tools/OPPL/
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25 4.- Copy oppl.xml, inference.xml and query.xml to
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26 /galaxy-dist/tools/OPPL/
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28 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
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30 <section name="Ontology Pre Processor Language" id="oppl">
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31 <tool file="OPPL/oppl.xml"/>
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32 <tool file="OPPL/inference.xml"/>
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33 <tool file="OPPL/query.xml"/>
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34 <tool file="OPPL/oppl_query.xml"/>
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35 </section>
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37 6.- Start Galaxy.
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41 FORESEEN FEATURES
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42 =================
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44 General (OPPL, Inference, Query, OPPL query):
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46 - Support for processing ontologies that import other ontologies loaded
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47 in galaxy.
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49 - Entities rendering definition (URI fragment, rdfs:label, QName, etc).
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51 - OWLLink and Racer support.
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54 OPPL:
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56 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
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57 cell).
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59 - Other output formats apart from RDF/XML.
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62 Inference:
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64 - Support for DataPropertyAssertion, DataPropertyHierarchy,
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65 DifferentIndividuals, ...
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67 OPPL query:
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71 KNOWN BUGS AND ISSUES
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72 =====================
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74 Currently Galaxy interprets any information thrown to stderr as a tool
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75 error, which is bad since OPPL (And many other tools) throw info to
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76 sdterr even if working properly. In OPPL Galaxy, stderr is redirected
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77 to /dev/null to avoid the problem, but that means that OPPL Galaxy does
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78 not fail gracefully (It simply stops). A wrapper will be implemented.
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80 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
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84 CONTACT
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85 =======
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87 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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91 ACKNOWLEDGEMENTS
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92 ================
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94 This work is funded by the Marie Curie Cofund program of the EU, FP7.
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98 COPYRIGHT AND LICENSE
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99 =====================
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100
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101 Copyright (c) 2011 Mikel Egaña Aranguren.
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103 (OPPL|Inference|Query)-Galaxy
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104 is free software: you can redistribute it and/or modify it under the
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105 terms of the GNU General Public License as published by the Free
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106 Software Foundation, either version 3 of the License, or (at your
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107 option) any later version.
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108
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109 This program is distributed in the hope that it will be useful,
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110 but WITHOUT ANY WARRANTY; without even the implied warranty of
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111 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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112 GNU General Public License for more details.
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113
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114 You should have received a copy of the GNU General Public License
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115 along with this program. If not, see <http://www.gnu.org/licenses/>.
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117 OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses.
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