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Added merge function and FaCT++ support. Improved OBO render
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Tue, 11 Oct 2011 11:09:52 +0200
parents 3740505b579c
children 14bfd77f8520
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7:756f1f5798bf 8:40adbcb2a7cc
10 INSTALLATION 10 INSTALLATION
11 ============ 11 ============
12 12
13 1.- Stop galaxy. 13 1.- Stop galaxy.
14 14
15 2.- Copy oppl_galaxy_tool.jar and oppl_galaxy_tool_lib/ to 15 2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/
16 /galaxy-dist/tool-data/shared/jars/. 16 and oppl_galaxy_tool_lib/ to /galaxy-dist/tool-data/shared/jars/.
17 17
18 3.- Create directory /galaxy-dist/tools/OPPL/. 18 3.- Create directory /galaxy-dist/tools/OPPL/.
19 19
20 4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/. 20 4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/.
21 21
41 Then execute the OPPL file against the OWL file: 41 Then execute the OPPL file against the OWL file:
42 42
43 Ontology Pre Processor Language 43 Ontology Pre Processor Language
44 >> Execute an OPPL file against an OWL file 44 >> Execute an OPPL file against an OWL file
45 45
46 An ontology produced by another galaxy tools can also be used
47
46 48
47 49
48 FORESEEN FEATURES 50 FORESEEN FEATURES
49 ================= 51 =================
50 52
51 Choose which inferred axioms to add to the output ontology (Right now 53 Choose which inferred axioms to add to the output ontology (Right now
52 only subsumption is available). 54 only subsumption between named classes is available).
53 55
54 FaCT++ and OWLLink support. 56 OWLLink support.
57
58
59
60 KNOWN BUGS AND ISSUES
61 =====================
62
63 Currently Galaxy interprets any information thrown to stderr as a tool
64 error, which is bad since OPPL (And many other tools) throw info to
65 sdterr even if working properly. In OPPL Galaxy, stderr is redirected to
66 /dev/null to avoid the problem, but that means that OPPL Galaxy does not
67 fail gracefully (It simply stops). A wrapper will be implemented.
68
69 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
70
71 OBO rendering does not work properly if the URIs lack the fragment or
72 if an object property lacks an rdfs:label.
55 73
56 74
57 75
58 TESTS 76 TESTS
59 ===== 77 =====
102 GNU General Public License for more details. 120 GNU General Public License for more details.
103 121
104 You should have received a copy of the GNU General Public License 122 You should have received a copy of the GNU General Public License
105 along with this program. If not, see <http://www.gnu.org/licenses/>. 123 along with this program. If not, see <http://www.gnu.org/licenses/>.
106 124
107 OPPL, OWL API and Pellet have their own licenses. 125 OPPL API, OWL API, Pellet, HermiT, FaCT++ and OBOformat have their own
126 licenses.
108 127
109 Galaxy is distributed as open source under the conditions of the 128 Galaxy is distributed as open source under the conditions of the
110 Academic Free License (http://www.opensource.org/licenses/academic.php). 129 Academic Free License (http://www.opensource.org/licenses/academic.php).
111 130
112 131