annotate NCBO_services/README @ 26:354aa87772e0

Uploaded
author jose-minyarro
date Mon, 19 Mar 2012 08:25:59 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
26
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
1
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
2
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
3
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
4 =============
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
5 NCBO Services
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
6 =============
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
7
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
8
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
9
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
10 INSTALLATION
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
11 ============
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
12
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
13 1.- Stop Galaxy.
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
14
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
15 2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
16
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
17 3.- Create directory /galaxy-dist/tools/NCBO_services/
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
18
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
19 4.- Copy the .xml files to /galaxy-dist/tools/NCBO_services/
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
20
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
21 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
22
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
23 <section name="NCBO services" id="NCBO_services">
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
24 <tool file="NCBO_services/get_ontology.xml"/>
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
25 <tool file="NCBO_services/extract.xml"/>
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
26 <tool file="NCBO_services/get_ontology_view.xml"/>
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
27 <tool file="NCBO_services/ncbo_annotator.xml"/>
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
28 <tool file="NCBO_services/ncbo_recommender.xml"/>
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
29 <tool file="NCBO_services/ncbo_search.xml"/>
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
30 <tool file="NCBO_services/ncbo_resourceIndex.xml"/>
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
31 </section>
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
32
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
33 6.- Start Galaxy.
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
34
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
35
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
36
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
37 USAGE
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
38 =====
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
39
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
40 Each tool has a different functionality, but all of them need a
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
41 bioportal API key. The API key can be obtained by creating an account at
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
42 bioportal (http://bioportal.bioontology.org/).
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
43
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
44
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
45
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
46 CONTACT
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
47 =======
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
48
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
49 Please send any request or comment to mikel.egana.aranguren@gmail.com or
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
50 jose.minya@gmail.com.
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
51
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
52
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
53
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
54 ACKNOWLEDGEMENTS
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
55 ================
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
56
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
57 The work on get_ontology, extract and get_ontology_view is funded by the
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
58 Marie Curie Cofund program of the EU, FP7.
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
59
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
60
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
61
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
62 COPYRIGHT AND LICENSE
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
63 =====================
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
64
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
65 get_ontology, extract and get_ontology_view are copyright of Mikel
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
66 EgaƱa Aranguren (2012), and they are distributed under a GPL 3 license
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
67 (http://www.gnu.org/licenses/)
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
68
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
69
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
70
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
71
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
72
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
73
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
74
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
75
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
76
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
77
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
78
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
79
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
80
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
81
354aa87772e0 Uploaded
jose-minyarro
parents:
diff changeset
82