diff OPPL/README @ 0:46b9d13a44fc

First commit (1.0.0)

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+++ b/OPPL/README	Tue Sep 06 14:53:59 2011 -0400
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+
+
+
+			===========
+			OPPL-GALAXY
+			===========
+
+
+
+INSTALLATION
+============
+
+1.- Stop galaxy.
+
+2.- Copy oppl_galaxy_tool.jar and oppl_galaxy_tool_lib/ to 
+/galaxy-dist/tool-data/shared/jars/.
+
+3.- Create directory /galaxy-dist/tools/OPPL/.
+
+4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/.
+
+5.- Add the following lines to /galaxy-dist/tool_conf.xml:
+
+  <section name="Ontology Pre Processor Language" id="oppl">
+    <tool file="OPPL/oppl.xml"/>
+  </section>
+
+6.- Start galaxy.
+
+Note that if you want you can use any java parameter by editing oppl.xml
+, eg: <command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 
+-jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL 
+> $output </command>
+
+
+
+USAGE
+=====
+
+An ontology and an OPPL file are needed (test.owl and test.oppl can be 
+used as samples). Load both:
+
+Get Data 
+	>> Upload File from your computer 
+
+Then execute the OPPL file against the OWL file: 
+
+Ontology Pre Processor Language
+	>> Execute an OPPL file against an OWL file 
+
+
+
+TESTS
+=====
+
+To run the functional test, first complete installation and then:
+
+1.- Copy test.owl and test.oppl to /galaxy-dist/test-data/
+
+2.- Add the following lines to /galaxy-dist/tool_conf.xml.sample
+
+  <section name="Ontology Pre Processor Language" id="oppl">
+    <tool file="OPPL/oppl.xml"/>
+  </section>
+
+3.- Execute /galaxy-dist/run_functional_tests.sh -id oppl
+
+
+
+CONTACT
+=======
+
+Please send any request or comment to [e-mail].
+
+
+
+ACKNOWLEDGEMENTS
+================
+
+This work is funded by the Marie Curie Cofund program of the EU, FP7.
+
+
+
+COPYRIGHT AND LICENSE
+=====================
+
+Copyright (c) 2011 Mikel Egaña Aranguren. 
+
+OPPL-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/>.
+
+OPPL, OWL API and Pellet have their own licenses.
+
+Galaxy is distributed as open source under the conditions of the 
+Academic Free License (http://www.opensource.org/licenses/academic.php).
+
+
+
+
+
+
+
+