diff OPPL/README @ 8:40adbcb2a7cc

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

--- a/OPPL/README	Sun Sep 18 12:57:22 2011 +0200
+++ b/OPPL/README	Tue Oct 11 11:09:52 2011 +0200
@@ -12,8 +12,8 @@
 
 1.- Stop galaxy.
 
-2.- Copy oppl_galaxy_tool.jar and oppl_galaxy_tool_lib/ to 
-/galaxy-dist/tool-data/shared/jars/.
+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/.
 
@@ -43,15 +43,33 @@
 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 is available).
+only subsumption between named classes is available).
+
+OWLLink support.
+
+
+
+KNOWN BUGS AND ISSUES
+=====================
 
-FaCT++ and OWLLink support.
+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.
 
 
 
@@ -104,7 +122,8 @@
 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.
+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).