view README @ 21:ffde1fafa066 draft

README corrected with proper installation instructions for mercurial (hg pull + hg update)

INSTALLATION VIA MERCURIAL (RECOMMENDED)
========================================

1.- Stop Galaxy.

2.- Move to galaxy-dist/tools/

3.- Clone the OPPL-Galaxy repository with mercurial: 

hg clone http://[e-mail]/repos/mikel-egana-aranguren/oppl

4.- Move to galaxy-dist/tools/oppl/ and run install.sh: 

chmod +x install.sh
./install.sh

5.- Add the following lines to /galaxy-dist/tool_conf.xml:

  <section name="Ontology Pre Processor Language" id="oppl">
    <tool file="oppl/oppl.xml"/>
    <tool file="oppl/inference.xml"/>
    <tool file="oppl/query.xml"/>
    <tool file="oppl/oppl_query.xml"/>
    <tool file="oppl/merge.xml"/>
  </section>

6.- Start Galaxy.

For updates: 

1.- Stop Galaxy.

2.- Move to galaxy-dist/tools/oppl/

3.- Pull changes adn update working copy: 

hg pull
hg update

4.- Run install.sh: 

./install.sh

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 the following files and directories to
/galaxy-dist/tool-data/shared/jars/:

oppl_galaxy_tool.jar
inference.jar
query.jar
oppl_query.jar
merge.jar
oppl_galaxy_lib/
inference_lib/
query_lib/
oppl_query_lib/
merge_lib/
FaCT++-linux-v1.5.2/ 
FaCT++-OSX-v1.5.2/
 
3.- Create directory /galaxy-dist/tools/oppl/

4.- Copy oppl.xml, inference.xml, query.xml, oppl_query.xml and 
merge.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"/>
    <tool file="oppl/inference.xml"/>
    <tool file="oppl/query.xml"/>
    <tool file="oppl/oppl_query.xml"/>
    <tool file="oppl/merge.xml"/>
  </section>

6.- Start Galaxy.



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

- Support for processing ontologies that import other ontologies loaded
in Galaxy (i.e. to resolve imports within galaxy).

- Entities rendering definition (URI fragment, rdfs:label, QName, etc).

- OWLLink and Racer support.

- Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
cell).

- Other output formats apart from RDF/XML.

- Support for DataPropertyAssertion, DataPropertyHierarchy,
DifferentIndividuals, ...



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



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|Inference|Query|OPPL-Query|Merge)-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, Elk and FaCT++ have their own licenses.