--- /dev/null
+###########################################################################################
+# #
+# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE #
+# #
+###########################################################################################
+
+### Properties supported by executables.
+### <execname> 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.<execname>.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.<execname>.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.<execname>.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.
+# <execname>.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.
+# <execname>.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.
+# <execname>.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.
+# <execname>.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;
+# <execname>.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.<execname>.bin,
+## local.<execname>.bin.windows properties are optional for these, if not
+## provided they will be replaced to the java executable path from JAVA_HOME
+## environmental variable.
+#<execname>.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
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