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Fix core WST file
[jabaws.git] / conf / Executable.properties
diff --git a/conf/Executable.properties b/conf/Executable.properties
index 7864ebf..4caf6c8 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -55,7 +55,7 @@
 ## local.<execname>.bin.windows properties are optional for these, if not \r
 ## provided they will be replaced to the java executable path from JAVA_HOME \r
 ## environmental variable. \r
-#<execname>.jar.file=binaries/windows/jronn3.1.jar\r
+#<execname>.jar.file=binaries/windows/bj3.0.4p-jronn.jar\r
 \r
   \r
 \r
@@ -69,22 +69,22 @@ 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 ram=6000M\r
 \r
 \r
 ######                 CLUSTAL OMEGA CONFIGURATION                ######\r
 local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe\r
 local.clustalo.bin=binaries/src/clustalo/src/clustalo\r
-cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo\r
+#cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo\r
 ## This parameters specifies the directory where the matrices files are stored   \r
 #clustalo.presets.file=conf/settings/ClustaloPresets.xml\r
 clustalo.parameters.file=conf/settings/ClustaloParameters.xml\r
-clustalo.limits.file=conf/settings/ClustaloLimits.xml\r
+#clustalo.limits.file=conf/settings/ClustaloLimits.xml\r
 ## ClustalO can be executed on multiple CPUs if run on the cluster. \r
 ## This parameter specifies the number of CPUs to use\r
-clustalo.cluster.cpunum=4\r
+#clustalo.cluster.cpunum=4\r
 ## This reserves a slot with CPUNUM on the cluster for the task\r
-clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  \r
+#clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00  \r
 \r
 \r
 ######                 MUSCLE CONFIGURATION                 ######\r
@@ -96,7 +96,7 @@ muscle.-matrix.path=binaries/matrices
 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 ram=6000M\r
 \r
 \r
 #####                  MAFFT CONFIGURATION                  ######\r
@@ -109,7 +109,7 @@ mafft.--aamatrix.path=binaries/matrices
 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 ram=6000M\r
 \r
 \r
 #####                  TCOFFEE CONFIGURATION                ######\r
@@ -124,7 +124,7 @@ tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml
 ## This parameter specifies the number of CPUs to use\r
 #tcoffee.cluster.cpunum=4\r
 ## This reserves a slot with CPUNUM on the cluster for the task\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
+#tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00  \r
 \r
 \r
 #####                  PROBCONS CONFIGURATION                ######\r
@@ -132,7 +132,7 @@ local.probcons.bin=binaries/src/probcons/probcons
 #cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons\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 ram=6000M\r
 \r
 \r
 #####                  JRONN CONFIGURATION                   ######\r
@@ -142,20 +142,21 @@ probcons.parameters.file=conf/settings/ProbconsParameters.xml
 #local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\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/windows/jronn3.1.jar\r
+#ERROR! jronn.jar.file=binaries/windows/jronn3.1.jar\r
+jronn.jar.file=binaries/windows/bj3.0.4p-jronn.jar\r
 #jronn.limits.file=conf/settings/JronnLimits.xml\r
 ## Jronn can use multiple CPUs\r
 ## This parameter specifies the number of CPU to use\r
 #jronn.cluster.cpunum=4\r
 ## This reserves a slot with CPUNUM on the cluster for the task\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
+#jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_cpu=24:00:00\r
 \r
 \r
 #####                  DISEMBL CONFIGURATION                 ###### \r
 local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
 #cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
 #disembl.limits.file=conf/settings/DisemblLimits.xml\r
-#disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#disembl.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 \r
 \r
 #####                  GLOBPLOT CONFIGURATION                ###### \r
@@ -163,7 +164,7 @@ local.globplot.bin=binaries/src/globplot/GlobPlot.py
 #cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
 #globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 \r
 globplot.limits.file=conf/settings/GlobPlotLimits.xml\r
-#globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#globplot.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 \r
 \r
 #####                  IUPRED CONFIGURATION                  ###### \r
@@ -175,7 +176,7 @@ iupred.bin.env=IUPred_PATH#binaries/src/iupred
 #cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred\r
 iupred.parameters.file=conf/settings/IUPredParameters.xml\r
 #iupred.limits.file=conf/settings/IUPredLimits.xml\r
-#iupred.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#iupred.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 \r
 \r
 #####                   AACON CONFIGURATION                  ######\r
@@ -192,4 +193,4 @@ aacon.presets.file=conf/settings/AAConPresets.xml
 ## This parameter specifies the number of CPUs to use\r
 #aacon.cluster.cpunum=4\r
 ## This reserves a slot with CPUNUM on the cluster for the task\r
-#aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r
+#aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00\r