-### 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
-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
-\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
-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
-\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
-mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\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
-\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
+### Properties supported by executables.\r
+### <execname> is one of the available applications: \r
+### [clustalw, mafft, muscle, propcons, tcoffee, iupred, jronn, globplot, disembl, aacon, jpred]\r
+\r
+### Path to the native executable on Windows must be either absolute, \r
+### 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
+### 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 = /home/jabaws/binaries/src/clustalw/src/clustalw2\r
+\r
+### At least one of the path to the native executable should be defined.\r
+\r
+### If an application supports presets, the preset file can have either \r
+### absolute or relative to the JABAWS web application path to the file. \r
+### The file is optional.\r
+# <execname>.presets.file = conf/settings/ClustalPresets.xml\r
+\r
+### If an application supports parameters, the parameter file can have either \r
+### absolute or relative to the JABAWS web application path to the file. \r
+### The file is 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
+## 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
+###########################################################################################\r
+# CLUSTAL W CONFIGURATION #\r
+###########################################################################################\r
+local.clustalw.bin.windows = binaries/windows/clustalw2.exe\r
+local.clustalw.bin = binaries/src/clustalw/src/clustalw2\r
+#cluster.clustalw.bin =/home/jabaws/binaries/src/clustalw/src/clustalw2\r
+### This parameter 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 ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# CLUSTAL OMEGA CONFIGURATION #\r
+###########################################################################################\r
+local.clustalo.bin.windows = binaries/windows/clustalo/clustalo.exe\r
+local.clustalo.bin = binaries/src/clustalo/src/clustalo\r
+#cluster.clustalo.bin = /home/jabaws/binaries/src/clustalo/src/clustalo\r
+### This parameter 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 run on multiple CPUs on the cluster. This parameter specifies CPU #NN\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
+###########################################################################################\r
+# MUSCLE CONFIGURATION #\r
+###########################################################################################\r
+local.muscle.bin.windows = binaries/windows/muscle.exe\r
+local.muscle.bin = binaries/src/muscle/muscle\r
+#cluster.muscle.bin = /home/jabaws/binaries/src/muscle/muscle\r
+### This parameter 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 ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# MAFFT CONFIGURATION #\r
+###########################################################################################\r
+local.mafft.bin = binaries/src/mafft/scripts/mafft\r
+#cluster.mafft.bin = /home/jabaws/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 ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# TCOFFEE CONFIGURATION #\r
+###########################################################################################\r
+local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee\r
+#cluster.tcoffee.bin = /home/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee\r