From: Sasha Sherstnev Date: Thu, 24 Oct 2013 11:43:29 +0000 (+0100) Subject: Remove security sensible configuration file X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a830419c63918f48a0da62f38ce7d0cb3f4a3ad5;p=jabaws.git Remove security sensible configuration file --- diff --git a/conf/Executable.properties.dundee b/conf/Executable.properties.dundee deleted file mode 100644 index 8d5c761..0000000 --- a/conf/Executable.properties.dundee +++ /dev/null @@ -1,212 +0,0 @@ -########################################################################################### -# # -# 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