Mercurial > repos > mikel-egana-aranguren > oppl
diff OPPL/oppl.xml @ 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
| author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Mon, 20 Aug 2012 11:39:56 +0200 |
| parents | 68c4ae500a13 |
| children | d3616fac4ca5 |
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--- a/OPPL/oppl.xml Thu Aug 02 09:22:57 2012 +0200 +++ b/OPPL/oppl.xml Mon Aug 20 11:39:56 2012 +0200 @@ -9,10 +9,10 @@ <!-- DEFAULT SETTINGS --> - <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> + <!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> <command> - java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null </command> @@ -23,7 +23,7 @@ <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> <!--<command> - java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null + java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null </commadn>--> @@ -34,7 +34,7 @@ <!-- For debugging simply remove 2>/dev/null Or uncomment bellow (And comment the default settings above). It will fail always (Due to OPPL messages) but at least it will be informative --> <!--<command> - java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output </command>--> @@ -56,7 +56,7 @@ <outputs> <data format="text" name="output" /> </outputs> - <tests> + <!--<tests> <test> <param name="input" value="test.owl"/> <param name="OPPL" value="test.oppl"/> @@ -64,7 +64,7 @@ <param name="reasoner" value="Pellet"/> <output name="out_file" file="test_new.owl"/> </test> - </tests> + </tests>--> <help> **About OPPL-Galaxy**