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New query tool added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Thu, 29 Mar 2012 14:49:22 +0200
parents 6ca67b155e32
children 622cde484f4c
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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_galaxy_lib/
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16 inference_lib/
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17 query_lib/
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18 FaCT++-linux-v1.5.2/
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19 FaCT++-OSX-v1.5.2/
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21 3.- Create directory /galaxy-dist/tools/OPPL/
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23 4.- Copy oppl.xml, inference.xml and query.xml to
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24 /galaxy-dist/tools/OPPL/
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26 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
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28 <section name="Ontology Pre Processor Language" id="oppl">
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29 <tool file="OPPL/oppl.xml"/>
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30 <tool file="OPPL/inference.xml"/>
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31 <tool file="OPPL/query.xml"/>
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32 </section>
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34 6.- Start Galaxy.
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38 FORESEEN FEATURES
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39 =================
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41 General (OPPL, Inference, Query):
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43 - Support for processing ontologies that import other ontologies loaded
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44 in galaxy.
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46 - Entities rendering definition (URI fragment, rdfs:label, QName, etc).
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48 - OWLLink and Racer support.
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51 OPPL:
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53 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
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54 cell).
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56 - Other output formats apart from RDF/XML.
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59 Inference:
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61 - Support for DataPropertyAssertion, DataPropertyHierarchy,
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62 DifferentIndividuals, ...
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66 KNOWN BUGS AND ISSUES
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67 =====================
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69 Currently Galaxy interprets any information thrown to stderr as a tool
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70 error, which is bad since OPPL (And many other tools) throw info to
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71 sdterr even if working properly. In OPPL Galaxy, stderr is redirected
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72 to /dev/null to avoid the problem, but that means that OPPL Galaxy does
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73 not fail gracefully (It simply stops). A wrapper will be implemented.
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75 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
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79 CONTACT
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80 =======
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82 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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86 ACKNOWLEDGEMENTS
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87 ================
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89 This work is funded by the Marie Curie Cofund program of the EU, FP7.
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93 COPYRIGHT AND LICENSE
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94 =====================
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96 Copyright (c) 2011 Mikel Egaña Aranguren.
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98 (OPPL|Inference|Query)-Galaxy
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99 is free software: you can redistribute it and/or modify it under the
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100 terms of the GNU General Public License as published by the Free
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101 Software Foundation, either version 3 of the License, or (at your
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102 option) any later version.
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104 This program is distributed in the hope that it will be useful,
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105 but WITHOUT ANY WARRANTY; without even the implied warranty of
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106 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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107 GNU General Public License for more details.
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108
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109 You should have received a copy of the GNU General Public License
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110 along with this program. If not, see <http://www.gnu.org/licenses/>.
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112 OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses.
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