X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=4caf6c80283831bd9363a488d72f2005733fa114;hb=acd285b98c4cfa54d2123861ffc30f2d42e86b20;hp=99b9c6c55dc60d57783c0079deb84bd5f87f2f31;hpb=ecb4bc6237a7407063f45e3044353e73a3bd1829;p=jabaws.git diff --git a/conf/Executable.properties b/conf/Executable.properties index 99b9c6c..4caf6c8 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -1,101 +1,196 @@ +################################################################################ +# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # +################################################################################ -### Clustal configuration ### -local.clustalw.bin.windows=binaries/clustalw2.exe +## 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 -# 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. +#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 h_vmem=6000M -l ram=6000M +#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/muscle.exe +###### MUSCLE CONFIGURATION ###### +local.muscle.bin.windows=binaries/windows/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! +#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 h_vmem=6000M -l ram=6000M +#muscle.limits.file=conf/settings/MuscleLimits.xml +#muscle.cluster.settings=-l h_cpu=24:00:00 -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 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 h_vmem=6000M -l ram=6000M +#mafft.limits.file=conf/settings/MafftLimits.xml +#mafft.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M + -### Tcoffee configuration ### +##### 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 +#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 +#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.windows= +##### 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! +#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 - -### 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= +#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.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 +#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 Tisean - GlobPlot and Disembl dependancy ### -#local.disembl.bin.windows= + +##### GLOBPLOT CONFIGURATION ###### 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 +#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 ###### +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 ### -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 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 -#TODO jronn.jvm.options=-Xms32M -Xmx512M -aacon.cluster.cpunum=4 +#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