X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=ec1b885a2d41de60c293c0ba8691636b0478f826;hb=dc8f4078acc94bd711079355d3cdf60dde467dae;hp=5433d777e92c1c5c26eb2c87f8f95ef8c720662a;hpb=e91343b74bb3c0b6ec3f792a08f2e981d7c50ad0;p=jabaws.git

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 5433d77..ec1b885 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -69,7 +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
+## 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 can be executed on multiple CPUs if run on the cluster. 
+## This parameter specifies the number of CPUs to use
+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 ram=1700M -l h_cpu=24:00:00  
 
 
 ######                 MUSCLE CONFIGURATION                 ######
@@ -81,7 +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                  ######
@@ -94,7 +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                ######
@@ -109,7 +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                ######
@@ -117,7 +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                   ######
@@ -133,14 +148,14 @@ jronn.jar.file=binaries/windows/jronn3.1.jar
 ## 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                ###### 
@@ -148,7 +163,7 @@ 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                  ###### 
@@ -160,7 +175,7 @@ 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                  ######
@@ -177,4 +192,4 @@ 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