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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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18:d3616fac4ca5 19:cc270db37d33
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4 MANUAL INSTALLATION
5 ============
6
7 1.- Stop Galaxy.
8
9 2.- Copy the following files and directories to
10 /galaxy-dist/tool-data/shared/jars/:
11
12 oppl_galaxy_tool.jar
13 inference.jar
14 query.jar
15 oppl_query.jar
16 merge.jar
17 oppl_galaxy_lib/
18 inference_lib/
19 query_lib/
20 oppl_query_lib/
21 merge_lib/
22 FaCT++-linux-v1.5.2/
23 FaCT++-OSX-v1.5.2/
24
25 3.- Create directory /galaxy-dist/tools/OPPL/
26
27 4.- Copy oppl.xml, inference.xml, query.xml, oppl_query.xml and
28 merge.xml to /galaxy-dist/tools/OPPL/
29
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">
33 <tool file="OPPL/oppl.xml"/>
34 <tool file="OPPL/inference.xml"/>
35 <tool file="OPPL/query.xml"/>
36 <tool file="OPPL/oppl_query.xml"/>
37 <tool file="OPPL/merge.xml"/>
38 </section>
39
40 6.- Start Galaxy.
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42
43 INSTALLATION VIA MERCURIAL AND SHELL SCRIPT
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45
46
47 FORESEEN FEATURES
48 =================
49
50 - Support for processing ontologies that import other ontologies loaded
51 in Galaxy (i.e. to resolve imports within galaxy).
52
53 - Entities rendering definition (URI fragment, rdfs:label, QName, etc).
54
55 - OWLLink and Racer support.
56
57 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
58 cell).
59
60 - Other output formats apart from RDF/XML.
61
62 - Support for DataPropertyAssertion, DataPropertyHierarchy,
63 DifferentIndividuals, ...
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65
66
67 KNOWN BUGS AND ISSUES
68 =====================
69
70 Currently Galaxy interprets any information thrown to stderr as a tool
71 error, which is bad since OPPL (And many other tools) throw info to
72 sdterr even if working properly. In OPPL Galaxy, stderr is redirected
73 to /dev/null to avoid the problem, but that means that OPPL Galaxy does
74 not fail gracefully (It simply stops). A wrapper will be implemented.
75
76 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
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78
79
80 CONTACT
81 =======
82
83 Please send any request or comment to mikel.egana.aranguren@gmail.com.
84
85
86
87 ACKNOWLEDGEMENTS
88 ================
89
90 This work is funded by the Marie Curie Cofund program of the EU, FP7.
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92
93
94 COPYRIGHT AND LICENSE
95 =====================
96
97 Copyright (c) 2011 Mikel Egaña Aranguren.
98
99 (OPPL|Inference|Query|OPPL-Query|Merge)-Galaxy
100 is free software: you can redistribute it and/or modify it under the
101 terms of the GNU General Public License as published by the Free
102 Software Foundation, either version 3 of the License, or (at your
103 option) any later version.
104
105 This program is distributed in the hope that it will be useful,
106 but WITHOUT ANY WARRANTY; without even the implied warranty of
107 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
108 GNU General Public License for more details.
109
110 You should have received a copy of the GNU General Public License
111 along with this program. If not, see <http://www.gnu.org/licenses/>.
112
113 OPPL API, OWL API, Pellet, HermiT, Elk and FaCT++ have their own licenses.
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115