annotate OPPL/README @ 8:40adbcb2a7cc

Added merge function and FaCT++ support. Improved OBO render

			===========
			OPPL-GALAXY
			===========



INSTALLATION
============

1.- Stop galaxy.

2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/ 
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.



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 

An ontology produced by another galaxy tools can also be used



FORESEEN FEATURES
=================

Choose which inferred axioms to add to the output ontology (Right now 
only subsumption between named classes is available).

OWLLink support.



KNOWN BUGS AND ISSUES
=====================

Currently Galaxy interprets any information thrown to stderr as a tool
error, which is bad since OPPL (And many other tools) throw info to 
sdterr even if working properly. In OPPL Galaxy, stderr is redirected to 
/dev/null to avoid the problem, but that means that OPPL Galaxy does not 
fail gracefully (It simply stops). A wrapper will be implemented.

http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr

OBO rendering does not work properly if the URIs lack the fragment or
if an object property lacks an rdfs:label.



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 API, OWL API, Pellet, HermiT, FaCT++ and OBOformat 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).