Mercurial > repos > mikel-egana-aranguren > oppl

annotate OPPL/README @ 11:6ca67b155e32

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Imports simplified, new tool for inference added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Fri, 09 Mar 2012 16:15:27 +0100
parents 3f31c0eb7539
children 7e6604a5ee55
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
1
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
2
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
3
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
4 INSTALLATION
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
5 ============
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
6
10
3f31c0eb7539 Interface improved
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 9
diff changeset
7 1.- Stop Galaxy.
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
8
11
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
9 2.- Copy the following files and dirs to
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
10 /galaxy-dist/tool-data/shared/jars/:
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
11
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
12 oppl_galaxy_tool.jar
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
13 oppl_galax_lib/
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
14 FaCT++-linux-v1.5.2/
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
15 FaCT++-OSX-v1.5.2/
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
16 inference.jar
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
17 inference_lib/
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
18
9
14bfd77f8520 Interface improved (Imports first) and proper handling of import/merge options added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 8
diff changeset
19 3.- Create directory /galaxy-dist/tools/OPPL/
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
20
11
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
21 4.- Copy oppl.xml and inference.xml to /galaxy-dist/tools/OPPL/
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
22
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
23 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
24
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
25 <section name="Ontology Pre Processor Language" id="oppl">
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
26 <tool file="OPPL/oppl.xml"/>
11
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
27 <tool file="OPPL/inference.xml"/>
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
28 </section>
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
29
10
3f31c0eb7539 Interface improved
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 9
diff changeset
30 6.- Start Galaxy.
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
31
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
32
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
33
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
34 FORESEEN FEATURES
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
35 =================
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
36
11
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
37 OPPL:
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
38
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
39 - Support for processing ontologies that import other ontologies loaded
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
40 in galaxy.
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
41
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
42 - Rendering definition (URI fragment, label, etc).
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
43
11
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
44 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
45 cell).
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
46
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
47 - OWLLink and Racer support.
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
48
10
3f31c0eb7539 Interface improved
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 9
diff changeset
49
11
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
50 Inference:
10
3f31c0eb7539 Interface improved
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 9
diff changeset
51
11
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
52 - DataPropertyAssertion, DataPropertyHierarchy, DifferentIndividuals,
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
53 ...
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
54
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
55
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
56
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
57
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
58 KNOWN BUGS AND ISSUES
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
59 =====================
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
60
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
61 Currently Galaxy interprets any information thrown to stderr as a tool
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
62 error, which is bad since OPPL (And many other tools) throw info to
11
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
63 sdterr even if working properly. In OPPL Galaxy, stderr is redirected
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
64 to /dev/null to avoid the problem, but that means that OPPL Galaxy does
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
65 not fail gracefully (It simply stops). A wrapper will be implemented.
8
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
66
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
67 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
40adbcb2a7cc Added merge function and FaCT++ support. Improved OBO render
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 6
diff changeset
68
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
69
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
70
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
71 CONTACT
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
72 =======
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
73
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
74 Please send any request or comment to mikel.egana.aranguren@gmail.com.
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
75
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
76
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
77
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
78 ACKNOWLEDGEMENTS
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
79 ================
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
80
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
81 This work is funded by the Marie Curie Cofund program of the EU, FP7.
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
82
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
83
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
84
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
85 COPYRIGHT AND LICENSE
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
86 =====================
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
87
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
88 Copyright (c) 2011 Mikel Egaña Aranguren.
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
89
11
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
90 (OPPL|Inference)-Galaxy is free software: you can redistribute it and/or
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
91 modify it under the terms of the GNU General Public License as published
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
92 by the Free Software Foundation, either version 3 of the License, or (at
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 10
diff changeset
93 your option) any later version.
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
94
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
95 This program is distributed in the hope that it will be useful,
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
96 but WITHOUT ANY WARRANTY; without even the implied warranty of
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
97 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
98 GNU General Public License for more details.
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
99
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
100 You should have received a copy of the GNU General Public License
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
101 along with this program. If not, see <http://www.gnu.org/licenses/>.
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
102
9
14bfd77f8520 Interface improved (Imports first) and proper handling of import/merge options added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 8
diff changeset
103 OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses.
0
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
104
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
105
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
106
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
107
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
108
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
109
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
110
46b9d13a44fc First commit (1.0.0)
mikel-egana-aranguren
parents:
diff changeset
111