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get_ontology jars included for simpler installation and README updated with installation information for new tools
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Wed, 18 Jan 2012 11:03:34 +0100
parents e25b2c00fffd
children 0078fe4c89e3
comparison
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3:097aa7000159 16:d3d6bdbcf3ea
10 INSTALLATION 10 INSTALLATION
11 ============ 11 ============
12 12
13 1.- Stop Galaxy. 13 1.- Stop Galaxy.
14 14
15 2.- Copy the .jar files and _lib/ directories to 15 2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/
16 /galaxy-dist/tool-data/shared/jars/
17 16
18 3.- Create directory /galaxy-dist/tools/NCBO_services/ 17 3.- Create directory /galaxy-dist/tools/NCBO_services/
19 18
20 4.- Copy get_ontology.xml to /galaxy-dist/tools/NCBO_services/ 19 4.- Copy the .xml files to /galaxy-dist/tools/NCBO_services/
21 20
22 5.- Add the following lines to /galaxy-dist/tool_conf.xml: 21 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
23 22
24 <section name="NCBO services" id="NCBO_services"> 23 <section name="NCBO services" id="NCBO_services">
25 <tool file="NCBO_services/get_ontology.xml"/> 24 <tool file="NCBO_services/get_ontology.xml"/>
25 <tool file="NCBO_services/ncbo_annotator.xml"/>
26 <tool file="NCBO_services/ncbo_annotator.xml"/>
27 <tool file="NCBO_services/ncbo_recommender.xml"/>
26 </section> 28 </section>
27 29
28 6.- Start Galaxy. 30 6.- Start Galaxy.
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32 USAGE 34 USAGE
33 ===== 35 =====
34 36
35 A bioportal API key and an ontology id must be provided. The API key can be 37 Each tool has a different functionality, but all of them need a
36 obtained by creating an account at bioportal 38 bioportal API key. The API key can be obtained by creating an account at
37 (http://bioportal.bioontology.org/). The id can be obtained in the ontology page 39 bioportal (http://bioportal.bioontology.org/).
38 (e.g. 1522 for BioPAX, see http://bioportal.bioontology.org/ontologies/1522)
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42 CONTACT 43 CONTACT
43 ======= 44 =======
44 45
45 Please send any request or comment to mikel.egana.aranguren@gmail.com. 46 Please send any request or comment to mikel.egana.aranguren@gmail.com or
46 47 jose.minya@gmail.com.
47
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49 ACKNOWLEDGEMENTS
50 ================
51
52 This work is funded by the Marie Curie Cofund program of the EU, FP7.
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56 COPYRIGHT AND LICENSE
57 =====================
58
59 Copyright (c) 2011 Mikel Egaña Aranguren.
60
61 NCBO Services is free software: you can redistribute it and/or modify
62 it under the terms of the GNU General Public License as published by
63 the Free Software Foundation, either version 3 of the License, or
64 (at your option) any later version.
65
66 This program is distributed in the hope that it will be useful,
67 but WITHOUT ANY WARRANTY; without even the implied warranty of
68 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
69 GNU General Public License for more details.
70
71 You should have received a copy of the GNU General Public License
72 along with this program. If not, see <http://www.gnu.org/licenses/>.
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