Mercurial > repos > mikel-egana-aranguren > oppl
annotate OPPL/README @ 5:68935f90c2db
Added OWL imports closure
| author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Sat, 17 Sep 2011 13:41:28 +0200 |
| parents | 4f60202c58d9 |
| children | 3740505b579c |
| rev | line source |
|---|---|
| 0 | 1 |
| 2 | |
| 3 | |
| 4 =========== | |
| 5 OPPL-GALAXY | |
| 6 =========== | |
| 7 | |
| 8 | |
| 9 | |
| 10 INSTALLATION | |
| 11 ============ | |
| 12 | |
| 13 1.- Stop galaxy. | |
| 14 | |
| 15 2.- Copy oppl_galaxy_tool.jar and oppl_galaxy_tool_lib/ to | |
| 16 /galaxy-dist/tool-data/shared/jars/. | |
| 17 | |
| 18 3.- Create directory /galaxy-dist/tools/OPPL/. | |
| 19 | |
| 20 4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/. | |
| 21 | |
| 22 5.- Add the following lines to /galaxy-dist/tool_conf.xml: | |
| 23 | |
| 24 <section name="Ontology Pre Processor Language" id="oppl"> | |
| 25 <tool file="OPPL/oppl.xml"/> | |
| 26 </section> | |
| 27 | |
| 28 6.- Start galaxy. | |
| 29 | |
| 30 Note that if you want you can use any java parameter by editing oppl.xml | |
| 31 , eg: <command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 | |
| 32 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL | |
|
3
5255f1333cc4
Version 1.0.1
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
0
diff
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33 $format > $output </command> |
| 0 | 34 |
| 35 | |
| 36 | |
| 37 USAGE | |
| 38 ===== | |
| 39 | |
| 40 An ontology and an OPPL file are needed (test.owl and test.oppl can be | |
| 41 used as samples). Load both: | |
| 42 | |
| 43 Get Data | |
| 44 >> Upload File from your computer | |
| 45 | |
| 46 Then execute the OPPL file against the OWL file: | |
| 47 | |
| 48 Ontology Pre Processor Language | |
| 49 >> Execute an OPPL file against an OWL file | |
| 50 | |
| 51 | |
|
5
68935f90c2db
Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
4
diff
changeset
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52 |
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4
4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
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53 FORESEEN FEATURES |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
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54 ================= |
|
4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
|
55 |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
|
56 Choose which inferred axioms to add to the output ontology (Right now |
|
4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
|
57 only subsumption is available). |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
|
58 |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
|
59 Choose reasoner (Right now only Pellet is available). |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
|
60 |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
|
61 |
| 0 | 62 |
| 63 TESTS | |
| 64 ===== | |
| 65 | |
| 66 To run the functional test, first complete installation and then: | |
| 67 | |
| 68 1.- Copy test.owl and test.oppl to /galaxy-dist/test-data/ | |
| 69 | |
| 70 2.- Add the following lines to /galaxy-dist/tool_conf.xml.sample | |
| 71 | |
| 72 <section name="Ontology Pre Processor Language" id="oppl"> | |
| 73 <tool file="OPPL/oppl.xml"/> | |
| 74 </section> | |
| 75 | |
| 76 3.- Execute /galaxy-dist/run_functional_tests.sh -id oppl | |
| 77 | |
| 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. | |
| 91 | |
| 92 | |
| 93 | |
| 94 COPYRIGHT AND LICENSE | |
| 95 ===================== | |
| 96 | |
| 97 Copyright (c) 2011 Mikel Egaña Aranguren. | |
| 98 | |
| 99 OPPL-Galaxy is free software: you can redistribute it and/or modify | |
| 100 it under the terms of the GNU General Public License as published by | |
| 101 the Free Software Foundation, either version 3 of the License, or | |
| 102 (at your option) any later version. | |
| 103 | |
| 104 This program is distributed in the hope that it will be useful, | |
| 105 but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 106 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| 107 GNU General Public License for more details. | |
| 108 | |
| 109 You should have received a copy of the GNU General Public License | |
| 110 along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 111 | |
| 112 OPPL, OWL API and Pellet have their own licenses. | |
| 113 | |
| 114 Galaxy is distributed as open source under the conditions of the | |
| 115 Academic Free License (http://www.opensource.org/licenses/academic.php). | |
| 116 | |
| 117 | |
| 118 | |
| 119 | |
| 120 | |
| 121 | |
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| 123 |