From cfeb0f2ed902dac482a1e1d113e19c7dd6d6b247 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Wed, 6 Jul 2011 12:13:54 +0000 Subject: [PATCH] Pre release Executable.properties, help added, unused properties commented out git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4393 e3abac25-378b-4346-85de-24260fe3988d --- conf/Executable.properties | 120 ++++++++++++++++++++++++++++++++------------ 1 file changed, 88 insertions(+), 32 deletions(-) diff --git a/conf/Executable.properties b/conf/Executable.properties index 5bd5b6e..4ce8e13 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -2,51 +2,94 @@ # THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # ################################################################################ -#File structure: +## Properties supported by all executables: -# 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 +## 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 -# Uncomment this if you want to limit the size of the job to be accepted by a WS +## 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 -# 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 +## 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 -# The number of CPU to use on the cluster by a Tcoffee -#tcoffee.cluster.cpunum=4 +## 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. #### -### Clustal configuration ### +## 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/jronn3.1.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. +## 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 -### Muscle configuration ### + +###### 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! +## 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 -### Mafft configuration ### + +##### 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 @@ -54,7 +97,7 @@ mafft.parameters.file=conf/settings/MafftParameters.xml #mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -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 # This variable is required by tcoffee @@ -62,55 +105,65 @@ 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 h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 -### Probcons configuration ### + +##### 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 ### -# If no local path are specified, Java is loaded from JAVA_HOME environment -# variable for local execution + +##### 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 jronn.jar.file=binaries/windows/jronn3.1.jar -jronn.limits.file=conf/settings/JronnLimits.xml +#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_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 -### Disembl configuration Tisean - Disembl dependancy ### +##### 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 -### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### + +##### 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 h_vmem=6000M -l ram=6000M -### IUPred configuration ### + +##### 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. +## 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 h_vmem=6000M -l ram=6000M -### AACon configuration ### + +##### 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 @@ -120,5 +173,8 @@ 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 h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 -- 1.7.10.2