diff OPPL/README @ 17:c9e01f86b07c draft

New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files

--- a/OPPL/README	Thu Aug 02 09:22:57 2012 +0200
+++ b/OPPL/README	Mon Aug 20 11:39:56 2012 +0200
@@ -6,24 +6,26 @@
 
 1.- Stop Galaxy.
 
-2.- Copy the following files and dirs to
+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 and query.xml to
-/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:
 
@@ -31,7 +33,8 @@
     <tool file="OPPL/oppl.xml"/>
     <tool file="OPPL/inference.xml"/>
     <tool file="OPPL/query.xml"/>
-    <tool file="OPPL/oppl_query.xml"/>   
+    <tool file="OPPL/oppl_query.xml"/>
+    <tool file="OPPL/merge.xml"/>
   </section>
 
 6.- Start Galaxy.
@@ -41,31 +44,21 @@
 FORESEEN FEATURES
 =================
 
-General (OPPL, Inference, Query, OPPL query):
-
 - Support for processing ontologies that import other ontologies loaded
-in galaxy.
+in galaxy (i.e. to resolve imports within galaxy).
 
 - Entities rendering definition (URI fragment, rdfs:label, QName, etc).
 
-- OWLLink and Racer support.
-
-
-OPPL:
+- OWLLink, Racer and ELK support.
 
 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
 cell).
 
 - Other output formats apart from RDF/XML.
 
-
-Inference:
-
 - Support for DataPropertyAssertion, DataPropertyHierarchy,
 DifferentIndividuals, ...
 
-OPPL query:
-
 
 
 KNOWN BUGS AND ISSUES
@@ -100,7 +93,7 @@
 
 Copyright (c) 2011 Mikel Egaña Aranguren. 
 
-(OPPL|Inference|Query)-Galaxy 
+(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
@@ -117,9 +110,3 @@
 OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses.
 
 
-
-
-
-
-
-