Remove security sensible configuration file

diff --git a/conf/Executable.properties.dundee b/conf/Executable.properties.dundee
deleted file mode 100644 (file)
index 8d5c761..0000000
--- a/conf/Executable.properties.dundee
+++ /dev/null
@@ -1,212 +0,0 @@
-###########################################################################################
-#                                                                                         #
-#            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