+################################################################################\r
+# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # \r
+################################################################################\r
\r
-### Clustal configuration ###\r
-local.clustalw.bin.windows=binaries/clustalw2.exe\r
+## Properties supported by all executables: \r
+\r
+## Path to the native executable on windows, \r
+## the path must be either absolute, or relative to JABAWS web application \r
+# local.<execname>.bin.windows=binaries/windows/clustalw2.exe\r
+\r
+## Path to the native executable not on windows (e.g. Linux, Mac)\r
+## the path must be either absolute, or relative to JABAWS web application\r
+# local.<execname>.bin=binaries/src/clustalw/src/clustalw2\r
+\r
+## Path to the native executable on the cluster (must be accessible from all \r
+## cluster nodes which will run JABAWS jobs). The path must be absolute. \r
+# cluster.<execname>.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2\r
+\r
+## At least one of the path to the native executable should be defined!\r
+ \r
+## Application supported presets, absolute or relative to \r
+## the JABAWS web application path to the file. Optional.\r
+# <execname>.presets.file=conf/settings/ClustalPresets.xml\r
+\r
+## Application supported parameters, absolute or relative to \r
+## the JABAWS web application path to the file. Optional. \r
+# <execname>.parameters.file=conf/settings/ClustalParameters.xml\r
+\r
+## Application limits, absolute or relative to \r
+## the JABAWS web application path to the file. Optional.\r
+## Use this if you want to limit the size of the job to be accepted by a \r
+## Webservice. The limits files we use in Dundee are provided with JABAWS. \r
+# <execname>.limits.file=conf/settings/ClustalLimits.xml\r
+\r
+## Flags passed to the cluster batch manager for the application. Optional.\r
+## This example sets a maximum execution time to 24 hours and maximum amount of \r
+## memory per task to 6Gb for SGE and OGE cluster batch managers.\r
+## Please note that all the examples of this parameter below are correct for \r
+## Sun Grid Engine or Open Grid Engine (untested) only! If you use a different \r
+## batch manager you would need to specify different flags. \r
+# <execname>.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+## Environmental variables required by native executables. Optional. \r
+## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2; \r
+#<execname>.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
+\r
+# Where <execname> is one of [clustalw, mafft, muscle, propcons, tcoffee,\r
+# iupred, jronn, globplot, disembl, aacon]\r
+\r
+\r
+### Parameters specific to the JAVA Jar executables. ### \r
+\r
+## Parameter supported by the executable Jar files, such as jronn and aacon, \r
+## point to the location of the jar file. Also, local.<execname>.bin, \r
+## local.<execname>.bin.windows properties are optional for these, if not \r
+## provided they will be replaced to the java executable path from JAVA_HOME \r
+## environmental variable. \r
+#<execname>.jar.file=binaries/windows/bj3.0.4p-jronn.jar\r
+\r
+ \r
+\r
+\r
+###### CLUSTAL CONFIGURATION ######\r
+local.clustalw.bin.windows=binaries/windows/clustalw2.exe\r
local.clustalw.bin=binaries/src/clustalw/src/clustalw2\r
-cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2\r
-# Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!\r
-# see engine.client.Util.getExecProperty() method for details \r
-# So they are case insensitive. \r
+#cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2\r
+## This parameters specifies the directory where the matrices files are stored \r
clustalw.-matrix.path=binaries/matrices\r
clustalw.presets.file=conf/settings/ClustalPresets.xml\r
clustalw.parameters.file=conf/settings/ClustalParameters.xml\r
-clustalw.limits.file=conf/settings/ClustalLimits.xml\r
-clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#clustalw.limits.file=conf/settings/ClustalLimits.xml\r
+#clustalw.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###### CLUSTAL OMEGA CONFIGURATION ######\r
+local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe\r
+local.clustalo.bin=binaries/src/clustalo/src/clustalo\r
+#cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo\r
+## This parameters specifies the directory where the matrices files are stored \r
+#clustalo.presets.file=conf/settings/ClustaloPresets.xml\r
+clustalo.parameters.file=conf/settings/ClustaloParameters.xml\r
+#clustalo.limits.file=conf/settings/ClustaloLimits.xml\r
+## ClustalO can be executed on multiple CPUs if run on the cluster. \r
+## This parameter specifies the number of CPUs to use\r
+#clustalo.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\r
+#clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 \r
+\r
\r
-### Muscle configuration ###\r
-local.muscle.bin.windows=binaries/muscle.exe\r
+###### MUSCLE CONFIGURATION ######\r
+local.muscle.bin.windows=binaries/windows/muscle.exe\r
local.muscle.bin=binaries/src/muscle/muscle\r
-# Beware version of muscle on the cluster older and does not support some \r
-# of the newer version attributed thus, will not work with Muscle.java wrapper!\r
-cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle\r
-#The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored\r
-# e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!\r
+#cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle\r
+## This parameters specifies the directory where the matrices files are stored\r
muscle.-matrix.path=binaries/matrices\r
muscle.presets.file=conf/settings/MusclePresets.xml\r
muscle.parameters.file=conf/settings/MuscleParameters.xml\r
-muscle.limits.file=conf/settings/MuscleLimits.xml\r
-muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#muscle.limits.file=conf/settings/MuscleLimits.xml\r
+#muscle.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
\r
-### Mafft configuration ###\r
-#local.mafft.bin.windows=\r
-local.mafft.bin=binaries/src/mafft/binaries/mafft\r
-cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/core/mafft\r
+\r
+##### MAFFT CONFIGURATION ######\r
+local.mafft.bin=binaries/src/mafft/scripts/mafft\r
+#cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft\r
+# These paths will be converted to absolute if relative.\r
mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
+## This parameters specifies the directory where the matrices files are stored\r
mafft.--aamatrix.path=binaries/matrices\r
mafft.presets.file=conf/settings/MafftPresets.xml\r
mafft.parameters.file=conf/settings/MafftParameters.xml\r
-mafft.limits.file=conf/settings/MafftLimits.xml\r
-mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#mafft.limits.file=conf/settings/MafftLimits.xml\r
+#mafft.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
+\r
\r
-### Tcoffee configuration ###\r
+##### TCOFFEE CONFIGURATION ######\r
local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee\r
-cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
-#/sw/bin/t_coffee\r
-# Sub matrix support does not work \r
-#tcoffee.-matrix.path=binaries/matrices\r
+#cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
# This variable is required by tcoffee\r
tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;\r
tcoffee.presets.file=conf/settings/TcoffeePresets.xml\r
tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml\r
-tcoffee.limits.file=conf/settings/TcoffeeLimits.xml\r
-tcoffee.cluster.cpunum=4\r
-tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 \r
+#tcoffee.limits.file=conf/settings/TcoffeeLimits.xml\r
+## Tcoffee can be executed on multiple CPUs if run on the cluster. \r
+## This parameter specifies the number of CPUs to use\r
+#tcoffee.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\r
+#tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 \r
+\r
\r
-### Probcons configuration ###\r
-#local.probcons.bin.windows=\r
+##### PROBCONS CONFIGURATION ######\r
local.probcons.bin=binaries/src/probcons/probcons\r
-cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons\r
-#Probcons does not support matrix loading - unrecognised option reported! \r
+#cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons\r
probcons.parameters.file=conf/settings/ProbconsParameters.xml\r
-probcons.limits.file=conf/settings/ProbconsLimits.xml\r
-probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
-\r
-### Jronn configuration ### \r
-local.jronn.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe \r
-local.jronn.bin=/sw/java/latest/bin/java\r
-cluster.jronn.bin=/sw/java/latest/bin/java\r
-jronn.jar.file=binaries/jronn3.1.jar\r
-jronn.parameters.file=conf/settings/JronnParameters.xml\r
-jronn.limits.file=conf/settings/JronnLimits.xml\r
-#TODO jronn.jvm.options=-Xms32M -Xmx512M\r
-jronn.cluster.cpunum=4\r
-jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r
-\r
-\r
-### Disembl configuration Tisean - Disembl dependancy ### \r
-#local.disembl.bin.windows= \r
+#probcons.limits.file=conf/settings/ProbconsLimits.xml\r
+#probcons.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+##### JRONN CONFIGURATION ######\r
+## If no local path is specified, Java is loaded from JAVA_HOME environment \r
+## variable for local execution. However, cluster.jronn.bin must be specified for \r
+## running Jronn on the cluster. \r
+#local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
+#local.jronn.bin=/sw/java/latest/bin/java\r
+#cluster.jronn.bin=/sw/java/latest/bin/java\r
+#ERROR! jronn.jar.file=binaries/windows/jronn3.1.jar\r
+jronn.jar.file=binaries/windows/bj3.0.4p-jronn.jar\r
+#jronn.limits.file=conf/settings/JronnLimits.xml\r
+## Jronn can use multiple CPUs\r
+## This parameter specifies the number of CPU to use\r
+#jronn.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\r
+#jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_cpu=24:00:00\r
+\r
+\r
+##### DISEMBL CONFIGURATION ###### \r
local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
-cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
-# disembl.parameters.file=conf/settings/DisemblParameters.xml\r
-disembl.limits.file=conf/settings/DisemblLimits.xml\r
-disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
+#disembl.limits.file=conf/settings/DisemblLimits.xml\r
+#disembl.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
\r
-### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### \r
-#local.disembl.bin.windows= \r
+\r
+##### GLOBPLOT CONFIGURATION ###### \r
local.globplot.bin=binaries/src/globplot/GlobPlot.py\r
-cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
-# globplot.parameters.file=conf/settings/GlobPlotParameters.xml\r
+#cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
+#globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 \r
globplot.limits.file=conf/settings/GlobPlotLimits.xml\r
-globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+#globplot.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+##### IUPRED CONFIGURATION ###### \r
+local.iupred.bin.windows=binaries/windows/iupred/iupred.exe \r
+local.iupred.bin=binaries/src/iupred/iupred\r
+## This must point to the directory where iupred binary is, with other files it \r
+## depends on. This path will be converted to absolute if relative at runtime. \r
+iupred.bin.env=IUPred_PATH#binaries/src/iupred\r
+#cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred\r
+iupred.parameters.file=conf/settings/IUPredParameters.xml\r
+#iupred.limits.file=conf/settings/IUPredLimits.xml\r
+#iupred.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
\r
\r
-### AACon configuration ###\r
-local.aacon.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe \r
-local.aacon.bin=/sw/java/latest/bin/java\r
-cluster.aacon.bin=/sw/java/latest/bin/java\r
-aacon.jar.file=binaries/aaconservation.jar\r
+##### AACON CONFIGURATION ######\r
+# This is just a path to the standard java executable \r
+#local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
+#local.aacon.bin=/sw/java/latest/bin/java\r
+#cluster.aacon.bin=/sw/java/latest/bin/java\r
+# Path to the AACon library\r
+aacon.jar.file=binaries/windows/aaconservation.jar\r
aacon.parameters.file=conf/settings/AAConParameters.xml\r
aacon.presets.file=conf/settings/AAConPresets.xml\r
-aacon.limits.file=conf/settings/AAConLimits.xml\r
-#TODO jronn.jvm.options=-Xms32M -Xmx512M\r
-aacon.cluster.cpunum=4\r
+#aacon.limits.file=conf/settings/AAConLimits.xml\r
+## AACon can use multiple CPUs\r
+## This parameter specifies the number of CPUs to use\r
+#aacon.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\r
+#aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00\r
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