Mercurial > repos > mikel-egana-aranguren > sparql_galaxy

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Reimplemented in Python, using RDFLib
author mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
date Fri, 25 Apr 2014 15:42:31 +0200
parents b8bf1af83841
children a0bb4dafb64b
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2:b8bf1af83841 3:24ad2706526c
1 INSTALLATION VIA TOOL-SHED 1 SPARQL-Galaxy
2 ========================== 2 =============
3 3
4 1.- Install through Admin >> Search and browse tool sheds 4 ABOUT
5 -----
5 6
6 2.- Copy SPARQLGalaxy.jar and SPARQLGalaxy_TEXT.jar to galaxy-dist/tool-data/shared/jars/ 7 Execute SPARQL queries against RDF datasets in Galaxy.
7 8
8 9
9 INSTALLATION VIA MERCURIAL 10 INSTALLATION
10 ========================== 11 ------------
11 12
12 1.- Stop Galaxy. 13 1. Stop Galaxy.
13 14
14 2.- Move to galaxy-dist/tools/ 15 2. Download or clone with mercurial (`hg clone http://mikel-egana-aranguren@toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/sparql_galaxy`).
15 16
16 3.- Clone the SPARQL-Galaxy repository with mercurial: 17 3. Copy everything under galaxy-dist/ to your server's galaxy-dist/ (i.e. recreate the tools/ and directory in your server).
17 18
18 hg clone http://mikel-egana-aranguren@toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/sparql_galaxy 19 4. Add the following lines to your server's /galaxy-dist/tool_conf.xml:
19 20
20 4.- Move to galaxy-dist/tools/sparql_galaxy and copy SPARQLGalaxy.jar and SPARQLGalaxy_TEXT.jar to galaxy-dist/tool-data/shared/jars/ 21 ```
21
22 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
23
24 <section name="SPARQL-Galaxy" id="SPARQLGalaxy"> 22 <section name="SPARQL-Galaxy" id="SPARQLGalaxy">
25 <tool file="sparql_galaxy/SPARQLGalaxy.xml"/> 23 <tool file="sparql_galaxy/SPARQLGalaxy.xml"/>
26 </section> 24 </section>
27 25 ```
28 6.- Start Galaxy. 26
29 27 5. Start Galaxy.
30 For updates:
31
32 1.- Stop Galaxy.
33
34 2.- Move to galaxy-dist/tools/sparql_galaxy/
35
36 3.- Pull changes and update working copy with mercurial:
37
38 hg pull
39 hg update
40
41 4.- Copy SPARQLGalaxy.jar to galaxy-dist/tool-data/shared/jars/
42
43 5.- Only edit galaxy-dist/tool_conf.xml in case a tool (an XML file) has been added/removed.
44
45 6.- Start Galaxy.
46
47
48
49 MANUAL INSTALLATION (DIRECT DOWNLOAD)
50 =====================================
51
52 Download and uncompress anywhere you like, and then:
53
54 1.- Stop Galaxy.
55
56 2.- Copy SPARQLGalaxy.jar and SPARQLGalaxy_TEXT.jar to galaxy-dist/tool-data/shared/jars/
57
58 3.- Create directory galaxy-dist/tools/sparql_galaxy/
59
60 4.- Copy SPARQLGalaxy.xml to galaxy-dist/tools/sparql_galaxy/
61
62 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
63
64 <section name="SPARQL-Galaxy" id="SPARQLGalaxy">
65 <tool file="sparql_galaxy/SPARQLGalaxy.xml"/>
66 </section>
67
68 6.- Start Galaxy.
69
70 28
71 29
72 CONTACT 30 CONTACT
73 ======= 31 -------
74 32
75 Please send any request or comment to mikel.egana.aranguren@gmail.com. 33 Please send any request or comment to mikel.egana.aranguren@gmail.com.
76 34
77 35
78
79 ACKNOWLEDGEMENTS 36 ACKNOWLEDGEMENTS
80 ================ 37 ----------------
81 38
82 This work is funded by the Marie Curie Cofund program of the EU, FP7, 39 This work is funded by the Marie Curie Cofund program of the EU, FP7,
83 and the Isaac Peral Program. 40 and the Genomic Resources group of the UPV-EHU.
84 41
85 42
86 43
87 COPYRIGHT AND LICENSE
88 =====================
89 44
90 Copyright (c) 2011 Mikel Egaña Aranguren, Alejandro Rodriguez Gonzalez
91
92 SPARQL-Galaxy is free software: you can redistribute it and/or modify it under the
93 terms of the GNU General Public License as published by the Free
94 Software Foundation, either version 3 of the License, or (at your
95 option) any later version.
96
97 This program is distributed in the hope that it will be useful,
98 but WITHOUT ANY WARRANTY; without even the implied warranty of
99 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
100 GNU General Public License for more details.
101
102 You should have received a copy of the GNU General Public License
103 along with this program. If not, see <http://www.gnu.org/licenses/>.
104
105 JENA has its own license.
106
107