X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=4caf6c80283831bd9363a488d72f2005733fa114;hb=HEAD;hp=7864ebf52c1b1848ac7fc557cc034db0a9f5f901;hpb=ff4eb72e1d1a381dc9317c80fcc1b92fc1c68d17;p=jabaws.git

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