From e69cb7b7bc6c5fe75779ebe053771a0a2f32fb3f Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Thu, 1 Aug 2013 18:18:13 +0100 Subject: [PATCH] JWS-67 Add Jpred to configuration files --- build.xml | 4 +- conf/Executable.properties | 362 ++++++++++++++++++++----------------- conf/Executable.properties.dundee | 212 ++++++++++++++++++++++ 3 files changed, 410 insertions(+), 168 deletions(-) create mode 100644 conf/Executable.properties.dundee diff --git a/build.xml b/build.xml index e0ad3a4..4fbafe9 100644 --- a/build.xml +++ b/build.xml @@ -19,7 +19,7 @@ - + @@ -80,7 +80,7 @@ - + diff --git a/conf/Executable.properties b/conf/Executable.properties index 9e2ccb4..c3d6e52 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -1,30 +1,36 @@ -################################################################################ -# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # -################################################################################ +########################################################################################### +# # +# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # +# # +########################################################################################### -## Properties supported by all executables: +### 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, -## the path must be either absolute, or relative to JABAWS web application -# local..bin.windows=binaries/windows/clustalw2.exe +### 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) -## the path must be either absolute, or relative to JABAWS web application -# local..bin=binaries/src/clustalw/src/clustalw2 +### 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=/homes/pvtroshin/workspace/jaba2/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! - -## Application supported presets, absolute or relative to -## the JABAWS web application path to the file. Optional. -# .presets.file=conf/settings/ClustalPresets.xml +### 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 -## Application supported parameters, absolute or relative to -## the JABAWS web application path to the file. Optional. -# .parameters.file=conf/settings/ClustalParameters.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. @@ -38,159 +44,183 @@ ## 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 +# .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. ### +# .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 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 +#.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 =/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=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee +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 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 +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 + +########################################################################################### +# MAFFT 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.settings = -l h_cpu=24:00:00 -l ram=6000M diff --git a/conf/Executable.properties.dundee b/conf/Executable.properties.dundee new file mode 100644 index 0000000..8d5c761 --- /dev/null +++ b/conf/Executable.properties.dundee @@ -0,0 +1,212 @@ +########################################################################################### +# # +# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # +# # +########################################################################################### + +### 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 CONFIGURATION # +########################################################################################### +local.clustalw.bin.windows = binaries/windows/clustalw2.exe +local.clustalw.bin = binaries/src/clustalw/src/clustalw2 +cluster.clustalw.bin = /home/jabaws/tomcat/webapps/jabaws/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 = -P webservices -R y -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/tomcat/webapps/jabaws/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. This parameter specifies the number of CPUs: +clustalo.cluster.cpunum = 4 +### This reserves a slot with CPUNUM on the cluster for the task +clustalo.cluster.settings = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l ram=3400M -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/tomcat/webapps/jabaws/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 = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M + + +########################################################################################### +# MAFFT CONFIGURATION # +########################################################################################### +local.mafft.bin = binaries/src/mafft/scripts/mafft +cluster.mafft.bin = /home/jabaws/tomcat/webapps/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 = -P webservices -R y -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/tomcat/webapps/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 can be executed on multiple CPUs. This parameter specifies the number of CPUs: +tcoffee.cluster.cpunum = 4 +### This reserves a slot with CPUNUM on the cluster for the task +tcoffee.cluster.settings = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l ram=3400M -l h_cpu=24:00:00 + + +########################################################################################### +# PROBCONS CONFIGURATION # +########################################################################################### +local.probcons.bin = binaries/src/probcons/probcons +cluster.probcons.bin = /home/jabaws/tomcat/webapps/jabaws/binaries/src/probcons/probcons +probcons.parameters.file = conf/settings/ProbconsParameters.xml +probcons.limits.file = conf/settings/ProbconsLimits.xml +probcons.cluster.settings = -P webservices -R y -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 = /home/jabaws/java/jdk/bin/java +cluster.jronn.bin = /home/jabaws/java/jdk/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 CPU: +jronn.cluster.cpunum = 4 +### This reserves a slot with CPUNUM on the cluster for the task +jronn.cluster.settings = -P webservices -R y -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/tomcat/webapps/jabaws/binaries/src/disembl/DisEMBL.py +disembl.limits.file = conf/settings/DisemblLimits.xml +disembl.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M + + +########################################################################################### +# GLOBPLOT CONFIGURATION # +########################################################################################### +local.globplot.bin = binaries/src/globplot/GlobPlot.py +cluster.globplot.bin = /home/jabaws/tomcat/webapps/jabaws/binaries/src/globplot/GlobPlot.py +globplot.bin.env = PYTHONPATH#/home/jabaws/tomcat/webapps/jabaws/binaries/src/globplot/biopython-1.50 +globplot.limits.file = conf/settings/GlobPlotLimits.xml +globplot.cluster.settings = -P webservices -R y -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/tomcat/webapps/jabaws/binaries/src/iupred/iupred +iupred.parameters.file = conf/settings/IUPredParameters.xml +iupred.limits.file = conf/settings/IUPredLimits.xml +iupred.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M + + +########################################################################################### +# AACON CONFIGURATION # +########################################################################################### +### This is just a path to the standard java executable +local.aacon.bin = /home/jabaws/java/jdk/bin/java +cluster.aacon.bin = /home/jabaws/java/jdk/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 = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l ram=3400M -l h_cpu=24:00:00 -- 1.7.10.2