Mercurial > repos > mikel-egana-aranguren > ncbo_services

comparison README @ 28:ebf11126df7c draft default tip

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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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27:e2b16720ef25 28:ebf11126df7c
1 INSTALLATION VIA MERCURIAL (RECOMMENDED)
2 ========================================
3
4 1.- Stop Galaxy.
5
6 2.- Move to galaxy-dist/tools/
7
8 3.- Clone the OPPL-Galaxy repository with mercurial:
9
10 hg clone http://mikel-egana-aranguren@toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/ncbo_services
11
12 3.- Move to galaxy-dist/tools/ncbo_services/ and copy the .jar files to /galaxy-dist/tool-data/shared/jars/
13
14 4.- Add the following lines to /galaxy-dist/tool_conf.xml:
15
16 <section name="NCBO services" id="ncbo_services">
17 <tool file="ncbo_services/get_ontology.xml"/>
18 <tool file="ncbo_services/extract.xml"/>
19 <tool file="ncbo_services/get_ontology_view.xml"/>
20 <tool file="ncbo_services/ncbo_annotator.xml"/>
21 <tool file="ncbo_services/ncbo_annotator.xml"/>
22 <tool file="ncbo_services/ncbo_recommender.xml"/>
23 </section>
24
25 5.- Start Galaxy.
26
27 For updates:
28
29 1.- Stop Galaxy.
30
31 2.- Move to galaxy-dist/tools/ncbo_services/
32
33 3.- Pull changes and update working copy:
34
35 hg pull
36 hg update
37
38 4.- Copy any new *.jar file to /galaxy-dist/tool-data/shared/jars/
39
40 5.- Only edit /galaxy-dist/tool_conf.xml in case a tool (an XML file) has been added/removed.
41
42 6.- Start Galaxy.
1 43
2 44
3 45
4 ============= 46 MANUAL INSTALLATION (DIRECT DOWNLOAD)
5 NCBO Services 47 =====================================
6 =============
7
8
9
10 INSTALLATION
11 ============
12 48
13 1.- Stop Galaxy. 49 1.- Stop Galaxy.
14 50
15 2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/ 51 2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/
16 52
17 3.- Create directory /galaxy-dist/tools/NCBO_services/ 53 3.- Create directory /galaxy-dist/tools/ncbo_services/
18 54
19 4.- Copy the .xml files to /galaxy-dist/tools/NCBO_services/ 55 4.- Copy the .xml files to /galaxy-dist/tools/ncbo_services/
20 56
21 5.- Add the following lines to /galaxy-dist/tool_conf.xml: 57 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
22 58
23 <section name="NCBO services" id="NCBO_services"> 59 <section name="NCBO services" id="ncbo_services">
24 <tool file="NCBO_services/get_ontology.xml"/> 60 <tool file="ncbo_services/get_ontology.xml"/>
25 <tool file="NCBO_services/extract.xml"/> 61 <tool file="ncbo_services/extract.xml"/>
26 <tool file="NCBO_services/get_ontology_view.xml"/> 62 <tool file="ncbo_services/get_ontology_view.xml"/>
27 <tool file="NCBO_services/ncbo_annotator.xml"/> 63 <tool file="ncbo_services/ncbo_annotator.xml"/>
28 <tool file="NCBO_services/ncbo_recommender.xml"/> 64 <tool file="ncbo_services/ncbo_annotator.xml"/>
29 <tool file="NCBO_services/ncbo_search.xml"/> 65 <tool file="ncbo_services/ncbo_recommender.xml"/>
30 <tool file="NCBO_services/ncbo_resourceIndex.xml"/>
31 </section> 66 </section>
32 67
33 6.- Start Galaxy. 68 6.- Start Galaxy.
34 69
35 70