################################################################################ # THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # ################################################################################ #File structure: # Uncomment this if you want to limit the size of the job to be accepted by a WS #clustalw.limits.file=conf/settings/ClustalLimits.xml # Uncomment this if you want to limit the size of the job to be accepted by a WS # Uncomment this if your what set a maximum execution time for this webservice # to 24 hours and maximum amount of memory per task to 6Gb. Please note that # you may need to change this if your cluster scheduler is not SGE or OGE. #mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M # The number of CPU to use on the cluster by a Tcoffee #tcoffee.cluster.cpunum=4 ### Clustal configuration ### local.clustalw.bin.windows=binaries/windows/clustalw2.exe local.clustalw.bin=binaries/src/clustalw/src/clustalw2 cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2 # Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison! # see engine.client.Util.getExecProperty() method for details # So they are case insensitive. 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 ### Muscle configuration ### local.muscle.bin.windows=binaries/windows/muscle.exe local.muscle.bin=binaries/src/muscle/muscle cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle #The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored # e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path! 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 ### Mafft configuration ### local.mafft.bin=binaries/src/mafft/scripts/mafft cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft # These paths will be converted to absolute if relative. mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34; 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 ### Tcoffee configuration ### local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee # This variable is required by tcoffee tcoffee.bin.env=HOME_4_TCOFFEE#jobsout; tcoffee.presets.file=conf/settings/TcoffeePresets.xml tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml #tcoffee.limits.file=conf/settings/TcoffeeLimits.xml #tcoffee.cluster.cpunum=4 #tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 ### Probcons configuration ### local.probcons.bin=binaries/src/probcons/probcons cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons #Probcons does not support matrix loading - unrecognised option reported! 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 ### Jronn configuration ### 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 jronn.limits.file=conf/settings/JronnLimits.xml #jronn.cluster.cpunum=4 #jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 ### Disembl configuration Tisean - Disembl dependancy ### 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 ### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### 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 ### IUPred configuration ### local.iupred.bin.windows=binaries/windows/iupred/iupred.exe local.iupred.bin=binaries/src/iupred/iupred # This must point to the directory where iupred binary is, with other files it depends on #iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred # This path will be converted to absolute if relative. 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 ### AACon configuration ### # This is just a path to the standard java executable local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe local.aacon.bin=/sw/java/latest/bin/java cluster.aacon.bin=/sw/java/latest/bin/java # Path to the AACon library aacon.jar.file=binaries/windows/aaconservation.jar aacon.parameters.file=conf/settings/AAConParameters.xml aacon.presets.file=conf/settings/AAConPresets.xml #aacon.limits.file=conf/settings/AAConLimits.xml #aacon.cluster.cpunum=4