annotate README @ 3:24ad2706526c draft

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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
1 SPARQL-Galaxy
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
2 =============
2
b8bf1af83841 Paste query added, query engine improved, examples added
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 1
diff changeset
3
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
4 ABOUT
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
5 -----
2
b8bf1af83841 Paste query added, query engine improved, examples added
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 1
diff changeset
6
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
7 Execute SPARQL queries against RDF datasets in Galaxy.
2
b8bf1af83841 Paste query added, query engine improved, examples added
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 1
diff changeset
8
b8bf1af83841 Paste query added, query engine improved, examples added
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents: 1
diff changeset
9
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
10 INSTALLATION
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
11 ------------
1
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
12
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
13 1. Stop Galaxy.
1
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
14
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
15 2. Download or clone with mercurial (`hg clone http://mikel-egana-aranguren@toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/sparql_galaxy`).
1
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
16
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
17 3. Copy everything under galaxy-dist/ to your server's galaxy-dist/ (i.e. recreate the tools/ and directory in your server).
1
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
18
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
19 4. Add the following lines to your server's /galaxy-dist/tool_conf.xml:
1
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
20
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
21 ```
1
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
22 <section name="SPARQL-Galaxy" id="SPARQLGalaxy">
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
23 <tool file="sparql_galaxy/SPARQLGalaxy.xml"/>
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
24 </section>
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
25 ```
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
26
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
27 5. Start Galaxy.
1
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
28
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
29
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
30 CONTACT
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
31 -------
1
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
32
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
33 Please send any request or comment to mikel.egana.aranguren@gmail.com.
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
34
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
35
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
36 ACKNOWLEDGEMENTS
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
37 ----------------
1
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
38
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
39 This work is funded by the Marie Curie Cofund program of the EU, FP7,
3
24ad2706526c Reimplemented in Python, using RDFLib
mikel-egana-aranguren <mikel.egana.aranguren@gmail.com>
parents: 2
diff changeset
40 and the Genomic Resources group of the UPV-EHU.
1
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
41
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
42
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
43
117a4b4c002d Added README but installation procedure not tested yet, pushed for backup
Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
44