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annotate README @ 19:cc270db37d33 draft

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Directories re-arranged
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sat, 06 Oct 2012 21:50:39 +0200
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children 46257c870179
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4 MANUAL 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 directories 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 merge.jar
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17 oppl_galaxy_lib/
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18 inference_lib/
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19 query_lib/
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20 oppl_query_lib/
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21 merge_lib/
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22 FaCT++-linux-v1.5.2/
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23 FaCT++-OSX-v1.5.2/
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25 3.- Create directory /galaxy-dist/tools/OPPL/
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27 4.- Copy oppl.xml, inference.xml, query.xml, oppl_query.xml and
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28 merge.xml to /galaxy-dist/tools/OPPL/
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30 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
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32 <section name="Ontology Pre Processor Language" id="oppl">
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33 <tool file="OPPL/oppl.xml"/>
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34 <tool file="OPPL/inference.xml"/>
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35 <tool file="OPPL/query.xml"/>
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36 <tool file="OPPL/oppl_query.xml"/>
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37 <tool file="OPPL/merge.xml"/>
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38 </section>
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40 6.- Start Galaxy.
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43 INSTALLATION VIA MERCURIAL AND SHELL SCRIPT
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47 FORESEEN FEATURES
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48 =================
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50 - Support for processing ontologies that import other ontologies loaded
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51 in Galaxy (i.e. to resolve imports within galaxy).
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53 - Entities rendering definition (URI fragment, rdfs:label, QName, etc).
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55 - OWLLink and Racer support.
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57 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
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58 cell).
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60 - Other output formats apart from RDF/XML.
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62 - Support for DataPropertyAssertion, DataPropertyHierarchy,
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63 DifferentIndividuals, ...
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67 KNOWN BUGS AND ISSUES
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68 =====================
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70 Currently Galaxy interprets any information thrown to stderr as a tool
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71 error, which is bad since OPPL (And many other tools) throw info to
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72 sdterr even if working properly. In OPPL Galaxy, stderr is redirected
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73 to /dev/null to avoid the problem, but that means that OPPL Galaxy does
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74 not fail gracefully (It simply stops). A wrapper will be implemented.
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76 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
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80 CONTACT
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81 =======
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82
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83 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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87 ACKNOWLEDGEMENTS
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88 ================
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89
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90 This work is funded by the Marie Curie Cofund program of the EU, FP7.
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94 COPYRIGHT AND LICENSE
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95 =====================
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97 Copyright (c) 2011 Mikel Egaña Aranguren.
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98
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99 (OPPL|Inference|Query|OPPL-Query|Merge)-Galaxy
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100 is free software: you can redistribute it and/or modify it under the
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101 terms of the GNU General Public License as published by the Free
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102 Software Foundation, either version 3 of the License, or (at your
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103 option) any later version.
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104
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105 This program is distributed in the hope that it will be useful,
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106 but WITHOUT ANY WARRANTY; without even the implied warranty of
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107 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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108 GNU General Public License for more details.
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109
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110 You should have received a copy of the GNU General Public License
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111 along with this program. If not, see <http://www.gnu.org/licenses/>.
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113 OPPL API, OWL API, Pellet, HermiT, Elk and FaCT++ have their own licenses.
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115