X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=dcb5d5a0aed1d94158b78d24d1a1fb7dac431b45;hb=55aac7dd80c4ae10829d89794ce297743cd152d5;hp=7471956543cdcd7304e68d883957cea4dbcb37bf;hpb=35947b9e0b6ae1be74f17d15cd6a65ceadc6d310;p=jabaws.git diff --git a/conf/Executable.properties b/conf/Executable.properties index 7471956..dcb5d5a 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -69,18 +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/clustalo -#cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/clustalo +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/ClustalPresets.xml -clustalo.parameters.file=conf/settings/ClustalParameters.xml -#clustalo.limits.file=conf/settings/ClustalLimits.xml -#clustalo.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M +#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 ###### @@ -92,7 +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 ###### @@ -105,7 +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 ###### @@ -120,7 +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 ###### @@ -128,7 +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 ###### @@ -144,14 +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 ###### @@ -159,7 +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 ###### @@ -171,7 +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 ###### @@ -188,4 +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