Mercurial > repos > mikel-egana-aranguren > ncbo_services

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Orain bai
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 08 Oct 2012 14:35:28 +0200
parents e2b16720ef25
children
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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1 INSTALLATION VIA MERCURIAL (RECOMMENDED)
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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2 ========================================
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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3
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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4 1.- Stop Galaxy.
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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5
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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6 2.- Move to galaxy-dist/tools/
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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7
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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8 3.- Clone the OPPL-Galaxy repository with mercurial:
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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9
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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10 hg clone http://mikel-egana-aranguren@toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/ncbo_services
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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12 3.- Move to galaxy-dist/tools/ncbo_services/ and copy the .jar files to /galaxy-dist/tool-data/shared/jars/
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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13
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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14 4.- Add the following lines to /galaxy-dist/tool_conf.xml:
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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15
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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16 <section name="NCBO services" id="ncbo_services">
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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17 <tool file="ncbo_services/get_ontology.xml"/>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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18 <tool file="ncbo_services/extract.xml"/>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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19 <tool file="ncbo_services/get_ontology_view.xml"/>
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20 <tool file="ncbo_services/ncbo_annotator.xml"/>
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21 <tool file="ncbo_services/ncbo_annotator.xml"/>
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22 <tool file="ncbo_services/ncbo_recommender.xml"/>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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23 </section>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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24
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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25 5.- Start Galaxy.
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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26
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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27 For updates:
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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29 1.- Stop Galaxy.
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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31 2.- Move to galaxy-dist/tools/ncbo_services/
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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33 3.- Pull changes and update working copy:
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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34
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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35 hg pull
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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36 hg update
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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38 4.- Copy any new *.jar file to /galaxy-dist/tool-data/shared/jars/
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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40 5.- Only edit /galaxy-dist/tool_conf.xml in case a tool (an XML file) has been added/removed.
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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41
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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42 6.- Start Galaxy.
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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46 MANUAL INSTALLATION (DIRECT DOWNLOAD)
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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47 =====================================
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49 1.- Stop Galaxy.
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50
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51 2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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53 3.- Create directory /galaxy-dist/tools/ncbo_services/
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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55 4.- Copy the .xml files to /galaxy-dist/tools/ncbo_services/
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57 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
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59 <section name="NCBO services" id="ncbo_services">
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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60 <tool file="ncbo_services/get_ontology.xml"/>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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61 <tool file="ncbo_services/extract.xml"/>
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parents: 27
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62 <tool file="ncbo_services/get_ontology_view.xml"/>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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63 <tool file="ncbo_services/ncbo_annotator.xml"/>
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parents: 27
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64 <tool file="ncbo_services/ncbo_annotator.xml"/>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 27
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65 <tool file="ncbo_services/ncbo_recommender.xml"/>
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66 </section>
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68 6.- Start Galaxy.
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72 USAGE
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73 =====
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75 Each tool has a different functionality, but all of them need a
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76 bioportal API key. The API key can be obtained by creating an account at
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77 bioportal (http://bioportal.bioontology.org/).
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81 CONTACT
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82 =======
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84 Please send any request or comment to mikel.egana.aranguren@gmail.com or
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85 jose.minya@gmail.com.
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89 ACKNOWLEDGEMENTS
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90 ================
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91
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92 The work on get_ontology, extract and get_ontology_view is funded by the
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93 Marie Curie Cofund program of the EU, FP7.
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97 COPYRIGHT AND LICENSE
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98 =====================
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99
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100 get_ontology, extract and get_ontology_view are copyright of Mikel
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101 Egaña Aranguren (2012), and they are distributed under a GPL 3 license
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102 (http://www.gnu.org/licenses/)
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