annotate NCBO_services/README @ 17:fc4c8a9b3152

branch merge
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Wed, 18 Jan 2012 11:06:11 +0100
parents d3d6bdbcf3ea
children 0078fe4c89e3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
1
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
2
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
3
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
4 =============
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
5 NCBO Services
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
6 =============
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
7
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
8
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
9
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
10 INSTALLATION
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
11 ============
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
12
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
13 1.- Stop Galaxy.
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
14
16
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
15 2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/
0
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
16
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
17 3.- Create directory /galaxy-dist/tools/NCBO_services/
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
18
16
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
19 4.- Copy the .xml files to /galaxy-dist/tools/NCBO_services/
0
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
20
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
21 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
22
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
23 <section name="NCBO services" id="NCBO_services">
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
24 <tool file="NCBO_services/get_ontology.xml"/>
16
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
25 <tool file="NCBO_services/ncbo_annotator.xml"/>
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
26 <tool file="NCBO_services/ncbo_annotator.xml"/>
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
27 <tool file="NCBO_services/ncbo_recommender.xml"/>
0
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
28 </section>
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
29
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
30 6.- Start Galaxy.
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
31
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
32
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
33
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
34 USAGE
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
35 =====
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
36
16
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
37 Each tool has a different functionality, but all of them need a
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
38 bioportal API key. The API key can be obtained by creating an account at
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
39 bioportal (http://bioportal.bioontology.org/).
0
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
40
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
41
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
42
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
43 CONTACT
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
44 =======
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
45
16
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
46 Please send any request or comment to mikel.egana.aranguren@gmail.com or
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
47 jose.minya@gmail.com.
0
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
48
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
49
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
50
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
51
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
52
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
53
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
54
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
55
e25b2c00fffd first version
mikel-egana-aranguren
parents:
diff changeset
56
16
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
57
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
58
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
59
d3d6bdbcf3ea get_ontology jars included for simpler installation and README updated with installation information for new tools
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 0
diff changeset
60