X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=a4f1aa3efaaf0d6f336e17c5607041016a31cd55;hb=5816a8c001f997198962a27d5d48cc7cf643520d;hp=99b9c6c55dc60d57783c0079deb84bd5f87f2f31;hpb=ecb4bc6237a7407063f45e3044353e73a3bd1829;p=jabaws.git diff --git a/conf/Executable.properties b/conf/Executable.properties index 99b9c6c..a4f1aa3 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -1,101 +1,255 @@ +########################################################################################### +# # +# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # +# # +########################################################################################### -### Clustal configuration ### -local.clustalw.bin.windows=binaries/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/muscle.exe -local.muscle.bin=binaries/src/muscle/muscle -# Beware version of muscle on the cluster older and does not support some -# of the newer version attributed thus, will not work with Muscle.java wrapper! -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.windows= -local.mafft.bin=binaries/src/mafft/binaries/mafft -cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/core/mafft -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 -#/sw/bin/t_coffee -# Sub matrix support does not work -#tcoffee.-matrix.path=binaries/matrices +### Properties supported by executables. +### is one of the available applications: +### [clustalw, mafft, muscle, propcons, tcoffee, iupred, jronn, globplot, disembl, aacon, jpred] + +### Path to the native executable on Windows 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) +### 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 = /home/jabaws/binaries/src/clustalw/src/clustalw2 + +### At least one of the path to the native executable should be defined. + +### If an application supports presets, the preset file can have either +### absolute or relative to the JABAWS web application path to the file. +### The file is optional. +# .presets.file = conf/settings/ClustalPresets.xml + +### If an application supports parameters, the parameter file can have either +### absolute or relative to the JABAWS web application path to the file. +### The file is 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; + +## 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 W CONFIGURATION # +########################################################################################### +local.clustalw.bin.windows = binaries/windows/clustalw2.exe +local.clustalw.bin = binaries/src/clustalw/src/clustalw2 +#cluster.clustalw.bin =/home/jabaws/binaries/src/clustalw/src/clustalw2 +### This parameter 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 = /home/jabaws/binaries/src/clustalo/src/clustalo +### This parameter 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 run on multiple CPUs on the cluster. This parameter specifies CPU #NN +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 = /home/jabaws/binaries/src/muscle/muscle +### This parameter 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 = /home/jabaws/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 = /home/jabaws/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.windows= -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_14\\bin\\java.exe -local.jronn.bin=/sw/java/latest/bin/java -cluster.jronn.bin=/sw/java/latest/bin/java -jronn.jar.file=binaries/jronn3.1.jar -jronn.parameters.file=conf/settings/JronnParameters.xml -jronn.limits.file=conf/settings/JronnLimits.xml -#TODO jronn.jvm.options=-Xms32M -Xmx512M -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.windows= -local.disembl.bin=binaries/src/disembl/DisEMBL.py -cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py -# disembl.parameters.file=conf/settings/DisemblParameters.xml -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.disembl.bin.windows= -local.globplot.bin=binaries/src/globplot/GlobPlot.py -cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py -# globplot.parameters.file=conf/settings/GlobPlotParameters.xml -globplot.limits.file=conf/settings/GlobPlotLimits.xml -globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M - - -### AACon configuration ### -local.aacon.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe -local.aacon.bin=/sw/java/latest/bin/java -cluster.aacon.bin=/sw/java/latest/bin/java -aacon.jar.file=binaries/aaconservation.jar -aacon.parameters.file=conf/settings/AAConParameters.xml -aacon.presets.file=conf/settings/AAConPresets.xml -aacon.limits.file=conf/settings/AAConLimits.xml -#TODO jronn.jvm.options=-Xms32M -Xmx512M -aacon.cluster.cpunum=4 +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 defines CPUs #N +#tcoffee.cluster.cpunum = 4 +### This paramer defines queue setting with CPUNUM on the cluster +#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 = /home/jabaws/binaries/src/probcons/probcons +probcons.parameters.file = conf/settings/ProbconsParameters.xml +probcons.limits.file = conf/settings/ProbconsLimits.xml +### This parameter defines queue settings for PROBCON on the cluster +#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 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 +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 CPUs +#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 = /home/jabaws/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 = /home/jabaws/binaries/src/globplot/GlobPlot.py +#globplot.bin.env = PYTHONPATH#/home/jabaws/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 = /home/jabaws/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 defines the number of CPUs: +#aacon.cluster.cpunum = 4 +### This parameter defines queue settings for AACON on the cluster +#aacon.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 + +########################################################################################### +# JPRED CONFIGURATION # +########################################################################################### +local.jpred.bin = binaries/src/jpred/jpred.pl +#cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl +# These paths will be converted to absolute if relative. +jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast;UNIREFDB#binaries/src/jpred/unirefdb; +### This parameters specifies the directory where the matrices files are stored +jpred.presets.file = conf/settings/JpredPresets.xml +jpred.parameters.file = conf/settings/JpredParameters.xml +jpred.limits.file = conf/settings/JpredLimits.xml +jpred.cluster.cpunum = 4 +#jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M + +########################################################################################### +# RNAALIFOLD CONFIGURATION # +########################################################################################### +local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe +local.rnaalifold.bin = binaries/src/ViennaRNA/Progs/RNAalifold +#cluster.rnaalifold.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/ViennaRNA/Progs/RNAalifold +rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml +rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml +rnaalifold.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M + +########################################################################################### +# MSAProbs CONFIGURATION # +########################################################################################### +local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs +cluster.msaprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs +msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml +msaprobs.limits.file = conf/settings/MSAprobsLimits.xml +msaprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M + +########################################################################################### +# GLprobs CONFIGURATION # +########################################################################################### +local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs +cluster.glprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/GLProbs-1.0/glprobs +glprobs.parameters.file = conf/settings/GLprobsParameters.xml +glprobs.limits.file = conf/settings/GLprobsLimits.xml +glprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M