From 19fd1455b9b55b62b888756d505167721520b4c3 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Mon, 27 Jun 2011 13:42:45 +0000 Subject: [PATCH] Generalizing configuration prior to release. git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4336 e3abac25-378b-4346-85de-24260fe3988d --- conf/Engine.cluster.properties | 5 +-- conf/Engine.local.properties | 7 ++-- conf/Executable.properties | 80 ++++++++++++++++++++------------------ conf/settings/AAConLimits.xml | 3 ++ conf/settings/ClustalLimits.xml | 13 +++---- conf/settings/MafftLimits.xml | 13 +++---- conf/settings/MuscleLimits.xml | 12 +++--- conf/settings/ProbconsLimits.xml | 8 ++-- conf/settings/TcoffeeLimits.xml | 15 ++++--- 9 files changed, 79 insertions(+), 77 deletions(-) diff --git a/conf/Engine.cluster.properties b/conf/Engine.cluster.properties index 344858b..caa2541 100644 --- a/conf/Engine.cluster.properties +++ b/conf/Engine.cluster.properties @@ -2,7 +2,7 @@ # enable or disable engine true | false # OPTIONAL defaults to false -engine.cluster.enable=true +engine.cluster.enable=false # Directory to use for temporary files storage # REQUIRED - cluster nodes must have access to this directory! @@ -12,8 +12,7 @@ engine.cluster.enable=true # to the job folders if this path is within JABA web application. # JABAWS statistic application just assume that the last name in the path is the # application folder in the root of JABAWS web application. -# cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout -cluster.tmp.directory=/homes/pvtroshin/workspace/jaba2/jobsout +cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout # Enable/disable cluster statistics collector cluster.stat.collector.enable=false diff --git a/conf/Engine.local.properties b/conf/Engine.local.properties index 25fd766..2f211e8 100644 --- a/conf/Engine.local.properties +++ b/conf/Engine.local.properties @@ -5,7 +5,8 @@ engine.local.enable=true # Directory to use for temporary files storage # OPTIONAL defaults to java temporary directory # Relative path within the project will be converted in absolute at runtime -local.tmp.directory=local_jobsout +# /cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout +local.tmp.directory=jobsout # Number of threads for tasks execution (valid values between 1 and 2x cpu. # Where x is a number of cores available in the system) @@ -14,8 +15,8 @@ local.tmp.directory=local_jobsout #engine.local.thread.number=3 # Enable/disable cluster statistics collector -local.stat.collector.enable=false +local.stat.collector.enable=true # Maximum amount of time the job is considered running in hours # Optional defaults to 24 hours -local.stat.maxruntime=6 \ No newline at end of file +local.stat.maxruntime=24 \ No newline at end of file diff --git a/conf/Executable.properties b/conf/Executable.properties index caf7355..d43ff97 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -1,3 +1,21 @@ +################################################################################ +# 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 @@ -9,25 +27,22 @@ cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/ 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 h_vmem=6000M -l ram=6000M ### 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! 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 h_vmem=6000M -l ram=6000M ### Mafft configuration ### -#local.mafft.bin.windows= 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. @@ -35,62 +50,52 @@ mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/ 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 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 # 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.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 +#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.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 +#jronn.parameters.file=conf/settings/JronnParameters.xml +#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.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 +#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 -# Dundee only settings -globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 -# 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 +#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 @@ -101,8 +106,8 @@ local.iupred.bin=binaries/src/iupred/iupred 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 +#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 @@ -113,6 +118,5 @@ cluster.aacon.bin=/sw/java/latest/bin/java 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.cluster.cpunum=4 diff --git a/conf/settings/AAConLimits.xml b/conf/settings/AAConLimits.xml index 5b066d9..5f9a482 100644 --- a/conf/settings/AAConLimits.xml +++ b/conf/settings/AAConLimits.xml @@ -10,6 +10,8 @@ 200 400 + + Quick conservation 10000 @@ -25,4 +27,5 @@ 2000 1000 + diff --git a/conf/settings/ClustalLimits.xml b/conf/settings/ClustalLimits.xml index 52b0ef3..ecb8148 100644 --- a/conf/settings/ClustalLimits.xml +++ b/conf/settings/ClustalLimits.xml @@ -2,21 +2,20 @@ compbio.runner.clustal.ClustalW - 100000 - 100000 + 1000 + 1000 # LocalEngineExecutionLimit # - 100000 - 100000 + 30 + 500 - - Disable gap weighting (Speed-oriented) 1000 3000 - --> + diff --git a/conf/settings/MafftLimits.xml b/conf/settings/MafftLimits.xml index 7067ff5..b3b3f81 100644 --- a/conf/settings/MafftLimits.xml +++ b/conf/settings/MafftLimits.xml @@ -2,17 +2,17 @@ compbio.runner.mafft.Mafft - 100000 - 100000 + 1000 + 1000 # LocalEngineExecutionLimit # - 100000 - 100000 + 20 + 500 - - + L-INS-i (Accuracy-oriented) 500 @@ -43,6 +43,5 @@ 2000 1000 - --> diff --git a/conf/settings/MuscleLimits.xml b/conf/settings/MuscleLimits.xml index 2aceb46..b08f536 100644 --- a/conf/settings/MuscleLimits.xml +++ b/conf/settings/MuscleLimits.xml @@ -2,17 +2,16 @@ compbio.runner.muscle.Muscle - 100000 - 100000 + 1000 + 1000 # LocalEngineExecutionLimit # - 100000 - 100000 + 20 + 500 - - Protein alignment(Fastest speed) 2000 @@ -28,6 +27,5 @@ 2000 3000 - --> diff --git a/conf/settings/ProbconsLimits.xml b/conf/settings/ProbconsLimits.xml index 1d871d7..e530fb9 100644 --- a/conf/settings/ProbconsLimits.xml +++ b/conf/settings/ProbconsLimits.xml @@ -2,12 +2,12 @@ compbio.runner.probcons.Probcons - 100000 - 100000 + 1000 + 1000 # LocalEngineExecutionLimit # - 100000 - 100000 + 20 + 500 diff --git a/conf/settings/TcoffeeLimits.xml b/conf/settings/TcoffeeLimits.xml index 660d27c..7e9dc9e 100644 --- a/conf/settings/TcoffeeLimits.xml +++ b/conf/settings/TcoffeeLimits.xml @@ -2,21 +2,20 @@ compbio.runner.tcoffee.Tcoffee - 100000 - 100000 + 1000 + 1000 # LocalEngineExecutionLimit # - 100000 - 100000 + 15 + 400 - - - Quick align. Very fast approximate (Speed-oriented) 1000 3000 - --> + -- 1.7.10.2