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comparison OPPL/README @ 9:14bfd77f8520

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Interface improved (Imports first) and proper handling of import/merge options added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Tue, 18 Oct 2011 10:30:16 +0200
parents 40adbcb2a7cc
children 3f31c0eb7539
comparison
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8:40adbcb2a7cc 9:14bfd77f8520
11 ============ 11 ============
12 12
13 1.- Stop galaxy. 13 1.- Stop galaxy.
14 14
15 2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/ 15 2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/
16 and oppl_galaxy_tool_lib/ to /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
22 5.- Add the following lines to /galaxy-dist/tool_conf.xml: 22 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
23 23
24 <section name="Ontology Pre Processor Language" id="oppl"> 24 <section name="Ontology Pre Processor Language" id="oppl">
25 <tool file="OPPL/oppl.xml"/> 25 <tool file="OPPL/oppl.xml"/>
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 46 An ontology produced by another galaxy tools can also be used.
47
48 Test.oppl and test.owl can be used as examples. More OPPL-Galaxy
49 examples can be obtained at http://miuras.inf.um.es/OPPL-Galaxy/, and
50 general OPPL script that may be useful to use with OPPL-Galaxy can be
51 obtained at http://oppl2.sourceforge.net/taggedexamples/.
47 52
48 53
49 54
50 FORESEEN FEATURES 55 FORESEEN FEATURES
51 ================= 56 =================
65 sdterr even if working properly. In OPPL Galaxy, stderr is redirected to 70 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 71 /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. 72 fail gracefully (It simply stops). A wrapper will be implemented.
68 73
69 http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr 74 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.
73 75
74 76
75 77
76 TESTS 78 TESTS
77 ===== 79 =====
120 GNU General Public License for more details. 122 GNU General Public License for more details.
121 123
122 You should have received a copy of the GNU General Public License 124 You should have received a copy of the GNU General Public License
123 along with this program. If not, see <http://www.gnu.org/licenses/>. 125 along with this program. If not, see <http://www.gnu.org/licenses/>.
124 126
125 OPPL API, OWL API, Pellet, HermiT, FaCT++ and OBOformat have their own 127 OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses.
126 licenses.
127
128 Galaxy is distributed as open source under the conditions of the
129 Academic Free License (http://www.opensource.org/licenses/academic.php).
130 128
131 129
132 130
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134 132