################################################################################ # THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # ################################################################################ ## Properties supported by all executables: ## Path to the native executable on windows, ## the path must be either absolute, or relative to JABAWS web application # local..bin.windows=binaries/windows/clustalw2.exe ## Path to the native executable not on windows (e.g. Linux, Mac) ## the path must be either absolute, or relative to JABAWS web application # local..bin=binaries/src/clustalw/src/clustalw2 ## Path to the native executable on the cluster (must be accessible from all ## cluster nodes which will run JABAWS jobs). The path must be absolute. # cluster..bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2 ## At least one of the path to the native executable should be defined! ## Application supported presets, absolute or relative to ## the JABAWS web application path to the file. Optional. # .presets.file=conf/settings/ClustalPresets.xml ## Application supported parameters, absolute or relative to ## the JABAWS web application path to the file. Optional. # .parameters.file=conf/settings/ClustalParameters.xml ## Application limits, absolute or relative to ## the JABAWS web application path to the file. Optional. ## Use this if you want to limit the size of the job to be accepted by a ## Webservice. The limits files we use in Dundee are provided with JABAWS. # .limits.file=conf/settings/ClustalLimits.xml ## Flags passed to the cluster batch manager for the application. Optional. ## This example sets a maximum execution time to 24 hours and maximum amount of ## memory per task to 6Gb for SGE and OGE cluster batch managers. ## Please note that all the examples of this parameter below are correct for ## Sun Grid Engine or Open Grid Engine (untested) only! If you use a different ## batch manager you would need to specify different flags. # .cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M ## Environmental variables required by native executables. Optional. ## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2; #.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34; # Where is one of [clustalw, mafft, muscle, propcons, tcoffee, # iupred, jronn, globplot, disembl, aacon] ### Parameters specific to the JAVA Jar executables. ### ## Parameter supported by the executable Jar files, such as jronn and aacon, ## point to the location of the jar file. Also, local..bin, ## local..bin.windows properties are optional for these, if not ## provided they will be replaced to the java executable path from JAVA_HOME ## environmental variable. #.jar.file=binaries/windows/bj3.0.4p-jronn.jar ###### 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 ## This parameters specifies the directory where the matrices files are stored 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 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 ###### 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 ## This parameters specifies the directory where the matrices files are stored 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 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; ## This parameters specifies the directory where the matrices files are stored 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 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 can be executed on multiple CPUs if run on the cluster. ## 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 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.parameters.file=conf/settings/ProbconsParameters.xml #probcons.limits.file=conf/settings/ProbconsLimits.xml #probcons.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M ##### JRONN CONFIGURATION ###### ## If no local path is specified, Java is loaded from JAVA_HOME environment ## variable for local execution. However, cluster.jronn.bin must be specified for ## running Jronn on the cluster. #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 #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_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 ram=6000M ##### GLOBPLOT CONFIGURATION ###### 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 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. This path will be converted to absolute if relative at runtime. 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 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 can use multiple CPUs ## 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 ram=1700M -l h_cpu=24:00:00