Add JRonn runner, tester, methods to parse jronn output files.

[jabaws.git] / conf / Executable.properties

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 681b3f0..cb3daa1 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -2,7 +2,7 @@
 ### Clustal configuration ###\r
 local.clustalw.bin.windows=binaries/clustalw2.exe\r
 local.clustalw.bin=binaries/src/clustalw/src/clustalw2\r
-#cluster.clustalw.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/src/clustalw2\r
+cluster.clustalw.bin=/homes/pvtroshin/workspace/JABA2/binaries/src/clustalw/src/clustalw2\r
 # Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!\r
 # see engine.client.Util.getExecProperty() method for details  \r
 # So they are case insensitive. \r
@@ -10,50 +10,61 @@ clustalw.-matrix.path=binaries/matrices
 clustalw.presets.file=conf/settings/ClustalPresets.xml\r
 clustalw.parameters.file=conf/settings/ClustalParameters.xml\r
 clustalw.limits.file=conf/settings/ClustalLimits.xml\r
-#clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
 \r
 ### Muscle configuration ###\r
 local.muscle.bin.windows=binaries/muscle.exe\r
 local.muscle.bin=binaries/src/muscle/muscle\r
 # Beware version of muscle on the cluster older and does not support some \r
 # of the newer version attributed thus, will not work with Muscle.java wrapper!\r
-cluster.muscle.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/muscle/muscle\r
+cluster.muscle.bin=/homes/pvtroshin/workspace/JABA2/binaries/src/muscle/muscle\r
 #The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored\r
 # e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!\r
 muscle.-matrix.path=binaries/matrices\r
 muscle.presets.file=conf/settings/MusclePresets.xml\r
 muscle.parameters.file=conf/settings/MuscleParameters.xml\r
 muscle.limits.file=conf/settings/MuscleLimits.xml\r
-#muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
 \r
 ### Mafft configuration ###\r
 #local.mafft.bin.windows=\r
 local.mafft.bin=binaries/src/mafft/binaries/mafft\r
-#cluster.mafft.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/mafft/core/mafft\r
+cluster.mafft.bin=/homes/pvtroshin/workspace/JABA2/binaries/src/mafft/core/mafft\r
 mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
 mafft.--aamatrix.path=binaries/matrices\r
 mafft.presets.file=conf/settings/MafftPresets.xml\r
 mafft.parameters.file=conf/settings/MafftParameters.xml\r
 mafft.limits.file=conf/settings/MafftLimits.xml\r
-#mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
 \r
 ### Tcoffee configuration ###\r
 local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee\r
-#cluster.tcoffee.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/tcoffee/t_coffee_source/t_coffee\r
+cluster.tcoffee.bin=/homes/pvtroshin/workspace/JABA2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
 #/sw/bin/t_coffee\r
 # Sub matrix support does not work \r
 #tcoffee.-matrix.path=binaries/matrices\r
 tcoffee.presets.file=conf/settings/TcoffeePresets.xml\r
 tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml\r
 tcoffee.limits.file=conf/settings/TcoffeeLimits.xml\r
-#tcoffee.cluster.cpunum=4\r
-#tcoffee.cluster.settings=-q mpi -pe mpi 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  \r
+tcoffee.cluster.cpunum=4\r
+tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  \r
 \r
 ### Probcons configuration ###\r
 #local.probcons.bin.windows=\r
 local.probcons.bin=binaries/src/probcons/probcons\r
-#cluster.probcons.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/probcons/probcons\r
+cluster.probcons.bin=/homes/pvtroshin/workspace/JABA2/binaries/src/probcons/probcons\r
 #Probcons does not support matrix loading - unrecognised option reported! \r
 probcons.parameters.file=conf/settings/ProbconsParameters.xml\r
 probcons.limits.file=conf/settings/ProbconsLimits.xml\r
-#probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+### Jronn configuration ### \r
+local.jronn.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe \r
+local.jronn.bin=/sw/java/latest/bin/java\r
+cluster.jronn.bin=/sw/java/latest/bin/java\r
+jronn.jar.file=binaries/jronn3.1.jar\r
+jronn.parameters.file=conf/settings/JronnParameters.xml\r
+jronn.limits.file=conf/settings/JronnLimits.xml\r
+jronn.jvm.options=-Xms32M -Xmx512M\r
+jronn.cluster.cpunum=4\r
+jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r