Mercurial > repos > mikel-egana-aranguren > sparql_galaxy
diff 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 |
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--- a/README Wed Dec 04 08:17:00 2013 +0100 +++ b/README Fri Apr 25 15:42:31 2014 +0200 @@ -1,107 +1,44 @@ -INSTALLATION VIA TOOL-SHED -========================== +SPARQL-Galaxy +============= -1.- Install through Admin >> Search and browse tool sheds +ABOUT +----- -2.- Copy SPARQLGalaxy.jar and SPARQLGalaxy_TEXT.jar to galaxy-dist/tool-data/shared/jars/ +Execute SPARQL queries against RDF datasets in Galaxy. -INSTALLATION VIA MERCURIAL -========================== +INSTALLATION +------------ -1.- Stop Galaxy. - -2.- Move to galaxy-dist/tools/ +1. Stop Galaxy. -3.- Clone the SPARQL-Galaxy repository with mercurial: +2. Download or clone with mercurial (`hg clone http://mikel-egana-aranguren@toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/sparql_galaxy`). -hg clone http://mikel-egana-aranguren@toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/sparql_galaxy +3. Copy everything under galaxy-dist/ to your server's galaxy-dist/ (i.e. recreate the tools/ and directory in your server). -4.- Move to galaxy-dist/tools/sparql_galaxy and copy SPARQLGalaxy.jar and SPARQLGalaxy_TEXT.jar to galaxy-dist/tool-data/shared/jars/ +4. Add the following lines to your server's /galaxy-dist/tool_conf.xml: -5.- Add the following lines to /galaxy-dist/tool_conf.xml: - +``` <section name="SPARQL-Galaxy" id="SPARQLGalaxy"> <tool file="sparql_galaxy/SPARQLGalaxy.xml"/> </section> - -6.- Start Galaxy. - -For updates: - -1.- Stop Galaxy. - -2.- Move to galaxy-dist/tools/sparql_galaxy/ - -3.- Pull changes and update working copy with mercurial: - -hg pull -hg update - -4.- Copy SPARQLGalaxy.jar to galaxy-dist/tool-data/shared/jars/ - -5.- Only edit galaxy-dist/tool_conf.xml in case a tool (an XML file) has been added/removed. - -6.- Start Galaxy. - - - -MANUAL INSTALLATION (DIRECT DOWNLOAD) -===================================== - -Download and uncompress anywhere you like, and then: - -1.- Stop Galaxy. - -2.- Copy SPARQLGalaxy.jar and SPARQLGalaxy_TEXT.jar to galaxy-dist/tool-data/shared/jars/ - -3.- Create directory galaxy-dist/tools/sparql_galaxy/ - -4.- Copy SPARQLGalaxy.xml to galaxy-dist/tools/sparql_galaxy/ - -5.- Add the following lines to /galaxy-dist/tool_conf.xml: - - <section name="SPARQL-Galaxy" id="SPARQLGalaxy"> - <tool file="sparql_galaxy/SPARQLGalaxy.xml"/> - </section> - -6.- Start Galaxy. - +``` + +5. Start Galaxy. CONTACT -======= +------- Please send any request or comment to mikel.egana.aranguren@gmail.com. - ACKNOWLEDGEMENTS -================ +---------------- This work is funded by the Marie Curie Cofund program of the EU, FP7, -and the Isaac Peral Program. +and the Genomic Resources group of the UPV-EHU. -COPYRIGHT AND LICENSE -===================== -Copyright (c) 2011 Mikel Egaña Aranguren, Alejandro Rodriguez Gonzalez - -SPARQL-Galaxy is free software: you can redistribute it and/or modify it under the -terms of the GNU General Public License as published by the Free -Software Foundation, either version 3 of the License, or (at your -option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see <http://www.gnu.org/licenses/>. - -JENA has its own license. - -