Mercurial > repos > mikel-egana-aranguren > oppl
annotate OPPL/README @ 9:14bfd77f8520
Interface improved (Imports first) and proper handling of import/merge options added
| author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
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| date | Tue, 18 Oct 2011 10:30:16 +0200 |
| parents | 40adbcb2a7cc |
| children | 3f31c0eb7539 |
| rev | line source |
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| 0 | 1 |
| 2 | |
| 3 | |
| 4 =========== | |
| 5 OPPL-GALAXY | |
| 6 =========== | |
| 7 | |
| 8 | |
| 9 | |
| 10 INSTALLATION | |
| 11 ============ | |
| 12 | |
| 13 1.- Stop galaxy. | |
| 14 | |
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15 2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/ |
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16 and oppl_galaxy_tool_lib/ to /galaxy-dist/tool-data/shared/jars/ |
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18 3.- Create directory /galaxy-dist/tools/OPPL/ |
| 0 | 19 |
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20 4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/ |
| 0 | 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 | |
| 31 | |
| 32 USAGE | |
| 33 ===== | |
| 34 | |
| 35 An ontology and an OPPL file are needed (test.owl and test.oppl can be | |
| 36 used as samples). Load both: | |
| 37 | |
| 38 Get Data | |
| 39 >> Upload File from your computer | |
| 40 | |
| 41 Then execute the OPPL file against the OWL file: | |
| 42 | |
| 43 Ontology Pre Processor Language | |
| 44 >> Execute an OPPL file against an OWL file | |
| 45 | |
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46 An ontology produced by another galaxy tools can also be used. |
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Interface improved (Imports first) and proper handling of import/merge options added
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parents:
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47 |
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Interface improved (Imports first) and proper handling of import/merge options added
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48 Test.oppl and test.owl can be used as examples. More OPPL-Galaxy |
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Interface improved (Imports first) and proper handling of import/merge options added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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49 examples can be obtained at http://miuras.inf.um.es/OPPL-Galaxy/, and |
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Interface improved (Imports first) and proper handling of import/merge options added
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parents:
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50 general OPPL script that may be useful to use with OPPL-Galaxy can be |
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Interface improved (Imports first) and proper handling of import/merge options added
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51 obtained at http://oppl2.sourceforge.net/taggedexamples/. |
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52 |
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54 |
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55 FORESEEN FEATURES |
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56 ================= |
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57 |
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58 Choose which inferred axioms to add to the output ontology (Right now |
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40adbcb2a7cc
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59 only subsumption between named classes is available). |
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40adbcb2a7cc
Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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60 |
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40adbcb2a7cc
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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61 OWLLink support. |
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40adbcb2a7cc
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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62 |
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40adbcb2a7cc
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
6
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63 |
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40adbcb2a7cc
Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
6
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64 |
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40adbcb2a7cc
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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65 KNOWN BUGS AND ISSUES |
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66 ===================== |
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parents:
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67 |
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parents:
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68 Currently Galaxy interprets any information thrown to stderr as a tool |
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40adbcb2a7cc
Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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69 error, which is bad since OPPL (And many other tools) throw info to |
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40adbcb2a7cc
Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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70 sdterr even if working properly. In OPPL Galaxy, stderr is redirected to |
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40adbcb2a7cc
Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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71 /dev/null to avoid the problem, but that means that OPPL Galaxy does not |
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40adbcb2a7cc
Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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72 fail gracefully (It simply stops). A wrapper will be implemented. |
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40adbcb2a7cc
Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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73 |
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40adbcb2a7cc
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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74 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr |
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40adbcb2a7cc
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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75 |
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76 |
| 0 | 77 |
| 78 TESTS | |
| 79 ===== | |
| 80 | |
| 81 To run the functional test, first complete installation and then: | |
| 82 | |
| 83 1.- Copy test.owl and test.oppl to /galaxy-dist/test-data/ | |
| 84 | |
| 85 2.- Add the following lines to /galaxy-dist/tool_conf.xml.sample | |
| 86 | |
| 87 <section name="Ontology Pre Processor Language" id="oppl"> | |
| 88 <tool file="OPPL/oppl.xml"/> | |
| 89 </section> | |
| 90 | |
| 91 3.- Execute /galaxy-dist/run_functional_tests.sh -id oppl | |
| 92 | |
| 93 | |
| 94 | |
| 95 CONTACT | |
| 96 ======= | |
| 97 | |
| 98 Please send any request or comment to mikel.egana.aranguren@gmail.com. | |
| 99 | |
| 100 | |
| 101 | |
| 102 ACKNOWLEDGEMENTS | |
| 103 ================ | |
| 104 | |
| 105 This work is funded by the Marie Curie Cofund program of the EU, FP7. | |
| 106 | |
| 107 | |
| 108 | |
| 109 COPYRIGHT AND LICENSE | |
| 110 ===================== | |
| 111 | |
| 112 Copyright (c) 2011 Mikel Egaña Aranguren. | |
| 113 | |
| 114 OPPL-Galaxy is free software: you can redistribute it and/or modify | |
| 115 it under the terms of the GNU General Public License as published by | |
| 116 the Free Software Foundation, either version 3 of the License, or | |
| 117 (at your option) any later version. | |
| 118 | |
| 119 This program is distributed in the hope that it will be useful, | |
| 120 but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 121 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| 122 GNU General Public License for more details. | |
| 123 | |
| 124 You should have received a copy of the GNU General Public License | |
| 125 along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 126 | |
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parents:
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127 OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses. |
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