From 2c116eabb17f6a2b80b9cf8d91770a7e67042fc1 Mon Sep 17 00:00:00 2001 From: =?utf8?q?F=C3=A1bio=20Madeira?= Date: Wed, 8 Mar 2017 16:11:10 +0000 Subject: [PATCH] Updated configs for testing local/cluster mode in the internal webservices2 boxe. --- conf/Engine.cluster.properties | 21 +- conf/Engine.local.properties | 15 +- conf/Executable.properties | 216 +++++++++---------- conf/Executable.properties.dundee | 145 ++++++------- dundee-conf/Engine.cluster.properties | 21 +- dundee-conf/Engine.local.properties | 17 +- dundee-conf/Executable.properties | 384 ++++++++++++++++++++++----------- dundee-conf/GA.properties | 18 ++ 8 files changed, 488 insertions(+), 349 deletions(-) create mode 100644 dundee-conf/GA.properties diff --git a/conf/Engine.cluster.properties b/conf/Engine.cluster.properties index 4cf86b2..cfae0dd 100644 --- a/conf/Engine.cluster.properties +++ b/conf/Engine.cluster.properties @@ -1,21 +1,22 @@ ################################################################################# # enable or disable engine true | false # OPTIONAL defaults to false -engine.cluster.enable=false +engine.cluster.enable=true ################################################################################# # Directory to use for temporary files storage # REQUIRED - cluster nodes must have access to this directory! -# WARNING!!! An absolute path is required +# WARNING!!! An absolute path is required # # Please note that statistic web application will only be able to generate links -# to the job folders if this path is within JABA web application. -# JABAWS statistic application just assume that the last name in the path is the -# application folder in the root of JABAWS web application. -cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout +# to the job folders if this path is within JABA web application. +# JABAWS statistic application just assume that the last name in the path is the +# application folder in the root of JABAWS web application. +#####cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout +cluster.tmp.directory=/homes/www-jws2/cluster_jobsout220 ################################################################################# -# Enable/disable cluster statistics collector +# Enable/disable cluster statistics collector cluster.stat.collector.enable=false # Frequency of statistics collecting (in minutes) # normal rate: once a date = 24 * 60 = 1440 @@ -23,14 +24,14 @@ cluster.stat.collector.update.frequency=1440 ################################################################################# # Maximum amount of time the job is considered running in hours -# Optional defaults to 7 days (168h) +# Optional defaults to 7 days (168h) cluster.stat.maxruntime=24 ################################################################################# -# Maximum amount of time the job directory is living (in hours), +# Maximum amount of time the job directory is living (in hours), # -1 means the directories are never deleted # Defaults is one week, i.e. 168 hours cluster.jobdir.maxlifespan=168 # Frequency of cleaning job directory (in minutes) # normal rate: once a date = 24 * 60 = 1440 -cluster.jobdir.cleaning.frequency=1 +cluster.jobdir.cleaning.frequency=1440 diff --git a/conf/Engine.local.properties b/conf/Engine.local.properties index dd2a0db..989ca5c 100644 --- a/conf/Engine.local.properties +++ b/conf/Engine.local.properties @@ -1,19 +1,20 @@ ################################################################################# # enable or disable engine true | false # OPTIONAL defaults to true -engine.local.enable=true +engine.local.enable=true ################################################################################# # Directory to use for temporary files storage # OPTIONAL defaults to java temporary directory # Relative path within the project will be converted in absolute at runtime #local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout -local.tmp.directory=jobsout +###local.tmp.directory=jobsout +local.tmp.directory=/homes/www-jws2/local_jobsout220 ################################################################################# -# Number of threads for tasks execution (valid values between 1 and 2x cpu. +# Number of threads for tasks execution (valid values between 1 and 2x cpu. # Where x is a number of cores available in the system) -# OPTIONAL defaults to the number of cores for core number <=4 and +# OPTIONAL defaults to the number of cores for core number <=4 and # number of cores-1 for greater core numbers engine.local.thread.number=2 @@ -26,13 +27,13 @@ local.stat.collector.update.frequency=1 # Maximum amount of time the job is considered running in hours # Optional defaults to 24 hours -local.stat.maxruntime=6 +local.stat.maxruntime=24 ################################################################################# -# Maximum amount of time the job directory is living (in hours), +# Maximum amount of time the job directory is living (in hours), # -1 means the directories are never deleted # Defaults is one week, i.e. 168 hours local.jobdir.maxlifespan=168 # Frequency of cleaning job directory (in minutes) # normal rate: once a date = 24 * 60 = 1440 -local.jobdir.cleaning.frequency=1 +local.jobdir.cleaning.frequency=1440 diff --git a/conf/Executable.properties b/conf/Executable.properties index 2bdc9a2..ac2fb9d 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -5,10 +5,10 @@ ########################################################################################### ### Properties supported by executables. -### is one of the available applications: +### 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, +### Path to the native executable on Windows must be either absolute, ### or relative to JABAWS web application # local..bin.windows = binaries/windows/clustalw2.exe @@ -16,212 +16,208 @@ ### 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. +### 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. +### 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. +### 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 +## 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. +## 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. +## 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; +## 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. +## 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 W CONFIGURATION # ########################################################################################### local.clustalw.bin.windows = binaries/windows/clustalw2.exe local.clustalw.bin = binaries/src/clustalw/src/clustalw2 -#cluster.clustalw.bin =/home/jabaws/binaries/src/clustalw/src/clustalw2 -### This parameter specifies the directory where the matrices files are stored +cluster.clustalw.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/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 =-l h_cpu=24:00:00 -l ram=6000M +clustalw.limits.file = conf/settings/ClustalLimits.xml +clustalw.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# CLUSTAL OMEGA CONFIGURATION # +# 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/binaries/src/clustalo/src/clustalo -### This parameter specifies the directory where the matrices files are stored +cluster.clustalo.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 run on multiple CPUs on the cluster. This parameter specifies CPU #NN +### 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 = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 +### This reserves a slot with CPUNUM on the Cluster for the task +clustalo.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M ########################################################################################### -# MUSCLE CONFIGURATION # +# MUSCLE CONFIGURATION # ########################################################################################### local.muscle.bin.windows = binaries/windows/muscle.exe local.muscle.bin = binaries/src/muscle/muscle -#cluster.muscle.bin = /home/jabaws/binaries/src/muscle/muscle -### This parameter specifies the directory where the matrices files are stored +cluster.muscle.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 = -l h_cpu=24:00:00 -l ram=6000M +muscle.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# MAFFT CONFIGURATION # +# MAFFT CONFIGURATION # ########################################################################################### -local.mafft.bin = binaries/src/mafft/scripts/mafft -#cluster.mafft.bin = /home/jabaws/binaries/src/mafft/scripts/mafft +local.mafft.bin = binaries/src/mafft/scripts/mafft +cluster.mafft.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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; +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 = -l h_cpu=24:00:00 -l ram=6000M +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 -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# TCOFFEE CONFIGURATION # +# TCOFFEE CONFIGURATION # ########################################################################################### -local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee -#cluster.tcoffee.bin = /home/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee +local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee +cluster.tcoffee.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 if run on the cluster. This parameter defines CPUs #N -#tcoffee.cluster.cpunum = 4 -### This paramer defines queue setting with CPUNUM on the cluster -#tcoffee.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 +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 -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M ########################################################################################### -# PROBCONS CONFIGURATION # +# PROBCONS CONFIGURATION # ########################################################################################### local.probcons.bin = binaries/src/probcons/probcons -#cluster.probcons.bin = /home/jabaws/binaries/src/probcons/probcons +cluster.probcons.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/probcons/probcons probcons.parameters.file = conf/settings/ProbconsParameters.xml probcons.limits.file = conf/settings/ProbconsLimits.xml -### This parameter defines queue settings for PROBCON on the cluster -#probcons.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +probcons.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# JRONN CONFIGURATION # +# 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 = /sw/java/latest/bin/java -#cluster.jronn.bin = /sw/java/latest/bin/java +### 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 = /homes/www-jws2/java/jdk/bin/java +cluster.jronn.bin = /homes/www-jws2/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 CPUs -#jronn.cluster.cpunum = 4 -### This reserves a slot with CPUNUM on the cluster for the task -#jronn.cluster.settings = -q 64bit-pri.q -pe smp 4 -l h_cpu=24:00:00 +### 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 -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# DISEMBL CONFIGURATION # +# DISEMBL CONFIGURATION # ########################################################################################### -local.disembl.bin = binaries/src/disembl/DisEMBL.py -#cluster.disembl.bin = /home/jabaws/binaries/src/disembl/DisEMBL.py -disembl.limits.file = conf/settings/DisemblLimits.xml -#disembl.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +local.disembl.bin = binaries/src/disembl/DisEMBL.py +cluster.disembl.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/disembl/DisEMBL.py +disembl.limits.file = conf/settings/DisemblLimits.xml +disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# GLOBPLOT CONFIGURATION # +# GLOBPLOT CONFIGURATION # ########################################################################################### -local.globplot.bin = binaries/src/globplot/GlobPlot.py -#cluster.globplot.bin = /home/jabaws/binaries/src/globplot/GlobPlot.py -#globplot.bin.env = PYTHONPATH#/home/jabaws/binaries/src/globplot/biopython-1.50 -globplot.limits.file = conf/settings/GlobPlotLimits.xml -#globplot.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +local.globplot.bin = binaries/src/globplot/GlobPlot.py +cluster.globplot.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/GlobPlot.py +globplot.bin.env = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/biopython-1.50 +globplot.limits.file = conf/settings/GlobPlotLimits.xml +globplot.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# IUPRED CONFIGURATION # +# IUPRED CONFIGURATION # ########################################################################################### -local.iupred.bin.windows = binaries/windows/iupred/iupred.exe +#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. +### 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/binaries/src/iupred/iupred +cluster.iupred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/iupred/iupred iupred.parameters.file = conf/settings/IUPredParameters.xml iupred.limits.file = conf/settings/IUPredLimits.xml -#iupred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +iupred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### -# AACON CONFIGURATION # +# AACON CONFIGURATION # ########################################################################################### -### This is just a path to the standard java executable -#local.aacon.bin.windows = D:\\Java\\jdk1.6.0_24\\bin\\java.exe -#local.aacon.bin = /sw/java/latest/bin/java -#cluster.aacon.bin = /sw/java/latest/bin/java +### This is just a path to the standard java executable +local.aacon.bin = /homes/www-jws2/java/jdk/bin/java +cluster.aacon.bin = /homes/www-jws2/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 defines the number of CPUs: -#aacon.cluster.cpunum = 4 -### This parameter defines queue settings for AACON on the cluster -#aacon.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 +### 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 -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M ########################################################################################### # JPRED CONFIGURATION # ########################################################################################### #local.jpred.bin = binaries/src/jpred/jpred.pl -##cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl +#cluster.jpred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/jpred/jpred.pl ## These paths will be converted to absolute if relative. #jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast ## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If ## you install the database to a different path chenge the variable here -#jpred.data.uniref.path = /data/UNIREFdb +#jpred.data.uniref.path = /homes/www-jpred/databases ## WARNING!!! ## Redefine jpred.data.uniref.name if you do undestand what the variable means #jpred.data.uniref.name = cluster @@ -230,32 +226,32 @@ aacon.limits.file = conf/settings/AAConLimits.xml #jpred.parameters.file = conf/settings/JpredParameters.xml #jpred.limits.file = conf/settings/JpredLimits.xml #jpred.cluster.cpunum = 4 -##jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +#jpred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=8000M ########################################################################################### # RNAALIFOLD CONFIGURATION # ########################################################################################### local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe local.rnaalifold.bin = binaries/src/ViennaRNA/Progs/RNAalifold -#cluster.rnaalifold.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/ViennaRNA/Progs/RNAalifold +cluster.rnaalifold.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/ViennaRNA/Progs/RNAalifold rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml -#rnaalifold.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +rnaalifold.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### # MSAProbs CONFIGURATION # ########################################################################################### local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs -#cluster.msaprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs +cluster.msaprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml msaprobs.limits.file = conf/settings/MSAprobsLimits.xml -#msaprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +msaprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### # GLprobs CONFIGURATION # ########################################################################################### local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs -#cluster.glprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/GLProbs-1.0/glprobs +cluster.glprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/GLProbs-1.0/glprobs glprobs.parameters.file = conf/settings/GLprobsParameters.xml glprobs.limits.file = conf/settings/GLprobsLimits.xml -#glprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +glprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M diff --git a/conf/Executable.properties.dundee b/conf/Executable.properties.dundee index fce1b21..079cded 100644 --- a/conf/Executable.properties.dundee +++ b/conf/Executable.properties.dundee @@ -1,14 +1,14 @@ ########################################################################################### # # -# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # +# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE FOR DUNDEE # # # ########################################################################################### ### Properties supported by executables. -### is one of the available applications: +### 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, +### Path to the native executable on Windows must be either absolute, ### or relative to JABAWS web application # local..bin.windows = binaries/windows/clustalw2.exe @@ -16,62 +16,59 @@ ### 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. +### 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. +### 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. +### 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 +## 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. +## 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. +## 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; +## 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. +## 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 # +# CLUSTAL W 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 +cluster.clustalw.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/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 +clustalw.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### @@ -79,15 +76,15 @@ clustalw.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### 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 +cluster.clustalo.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 +### This reserves a slot with CPUNUM on the Cluster for the task +clustalo.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M ########################################################################################### @@ -95,20 +92,20 @@ clustalo.cluster.settings = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l ram ########################################################################################### 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 +cluster.muscle.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 +muscle.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -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 +cluster.mafft.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 @@ -116,14 +113,14 @@ 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 +mafft.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -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 +cluster.tcoffee.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 @@ -131,75 +128,75 @@ 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 +### This reserves a slot with CPUNUM on the Cluster for the task +tcoffee.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M ########################################################################################### # PROBCONS CONFIGURATION # ########################################################################################### local.probcons.bin = binaries/src/probcons/probcons -cluster.probcons.bin = /home/jabaws/tomcat/webapps/jabaws/binaries/src/probcons/probcons +cluster.probcons.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 +probcons.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -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 +### 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 = /homes/www-jws2/java/jdk/bin/java +cluster.jronn.bin = /homes/www-jws2/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 +### This reserves a slot with CPUNUM on the Cluster for the task +jronn.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### # DISEMBL CONFIGURATION # ########################################################################################### local.disembl.bin = binaries/src/disembl/DisEMBL.py -cluster.disembl.bin = /home/jabaws/tomcat/webapps/jabaws/binaries/src/disembl/DisEMBL.py +cluster.disembl.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 +disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -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 +cluster.globplot.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/GlobPlot.py +globplot.bin.env = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 +globplot.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### # IUPRED CONFIGURATION # ########################################################################################### -local.iupred.bin.windows = binaries/windows/iupred/iupred.exe +#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. +### 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 +cluster.iupred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 +iupred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -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 +### This is just a path to the standard java executable +local.aacon.bin = /homes/www-jws2/java/jdk/bin/java +cluster.aacon.bin = /homes/www-jws2/java/jdk/bin/java ### Path to the AACon library aacon.jar.file = binaries/windows/aaconservation.jar aacon.parameters.file = conf/settings/AAConParameters.xml @@ -208,19 +205,19 @@ 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 +### This reserves a slot with CPUNUM on the Cluster for the task +aacon.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M ########################################################################################### # JPRED CONFIGURATION # ########################################################################################### #local.jpred.bin = binaries/src/jpred/jpred.pl -##cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl +#cluster.jpred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/jpred/jpred.pl ## These paths will be converted to absolute if relative. #jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast ## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If ## you install the database to a different path chenge the variable here -#jpred.data.uniref.path = /data/UNIREFdb +#jpred.data.uniref.path = /homes/www-jpred/databases ## WARNING!!! ## Redefine jpred.data.uniref.name if you do undestand what the variable means #jpred.data.uniref.name = cluster @@ -229,32 +226,32 @@ aacon.cluster.settings = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l ram=3 #jpred.parameters.file = conf/settings/JpredParameters.xml #jpred.limits.file = conf/settings/JpredLimits.xml #jpred.cluster.cpunum = 4 -##jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +#jpred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=8000M ########################################################################################### # RNAALIFOLD CONFIGURATION # ########################################################################################### local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe local.rnaalifold.bin = binaries/src/ViennaRNA/Progs/RNAalifold -cluster.rnaalifold.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/ViennaRNA/Progs/RNAalifold +cluster.rnaalifold.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/ViennaRNA/Progs/RNAalifold rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml -rnaalifold.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +rnaalifold.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### # MSAProbs CONFIGURATION # ########################################################################################### local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs -cluster.msaprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs +cluster.msaprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml msaprobs.limits.file = conf/settings/MSAprobsLimits.xml -msaprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +msaprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### # GLprobs CONFIGURATION # ########################################################################################### local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs -cluster.glprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/GLProbs-1.0/glprobs +cluster.glprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/GLProbs-1.0/glprobs glprobs.parameters.file = conf/settings/GLprobsParameters.xml glprobs.limits.file = conf/settings/GLprobsLimits.xml -glprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +glprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M diff --git a/dundee-conf/Engine.cluster.properties b/dundee-conf/Engine.cluster.properties index ffe09bf..cfae0dd 100644 --- a/dundee-conf/Engine.cluster.properties +++ b/dundee-conf/Engine.cluster.properties @@ -6,31 +6,32 @@ engine.cluster.enable=true ################################################################################# # Directory to use for temporary files storage # REQUIRED - cluster nodes must have access to this directory! -# WARNING!!! An absolute path is required +# WARNING!!! An absolute path is required # # Please note that statistic web application will only be able to generate links -# to the job folders if this path is within JABA web application. -# JABAWS statistic application just assume that the last name in the path is the -# application folder in the root of JABAWS web application. -cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout +# to the job folders if this path is within JABA web application. +# JABAWS statistic application just assume that the last name in the path is the +# application folder in the root of JABAWS web application. +#####cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout +cluster.tmp.directory=/homes/www-jws2/cluster_jobsout220 ################################################################################# -# Enable/disable cluster statistics collector -cluster.stat.collector.enable=true +# Enable/disable cluster statistics collector +cluster.stat.collector.enable=false # Frequency of statistics collecting (in minutes) # normal rate: once a date = 24 * 60 = 1440 cluster.stat.collector.update.frequency=1440 ################################################################################# # Maximum amount of time the job is considered running in hours -# Optional defaults to 7 days (168h) +# Optional defaults to 7 days (168h) cluster.stat.maxruntime=24 ################################################################################# -# Maximum amount of time the job directory is living (in hours), +# Maximum amount of time the job directory is living (in hours), # -1 means the directories are never deleted # Defaults is one week, i.e. 168 hours cluster.jobdir.maxlifespan=168 # Frequency of cleaning job directory (in minutes) # normal rate: once a date = 24 * 60 = 1440 -cluster.jobdir.cleaning.frequency=1 +cluster.jobdir.cleaning.frequency=1440 diff --git a/dundee-conf/Engine.local.properties b/dundee-conf/Engine.local.properties index 2ce1671..6093681 100644 --- a/dundee-conf/Engine.local.properties +++ b/dundee-conf/Engine.local.properties @@ -1,19 +1,20 @@ ################################################################################# # enable or disable engine true | false # OPTIONAL defaults to true -engine.local.enable=true +engine.local.enable=true ################################################################################# # Directory to use for temporary files storage # OPTIONAL defaults to java temporary directory # Relative path within the project will be converted in absolute at runtime -local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout -#local.tmp.directory=jobsout +#local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout +###local.tmp.directory=jobsout +local.tmp.directory=/homes/www-jws2/local_jobsout220 ################################################################################# -# Number of threads for tasks execution (valid values between 1 and 2x cpu. +# Number of threads for tasks execution (valid values between 1 and 2x cpu. # Where x is a number of cores available in the system) -# OPTIONAL defaults to the number of cores for core number <=4 and +# OPTIONAL defaults to the number of cores for core number <=4 and # number of cores-1 for greater core numbers engine.local.thread.number=2 @@ -26,13 +27,13 @@ local.stat.collector.update.frequency=1 # Maximum amount of time the job is considered running in hours # Optional defaults to 24 hours -local.stat.maxruntime=6 +local.stat.maxruntime=24 ################################################################################# -# Maximum amount of time the job directory is living (in hours), +# Maximum amount of time the job directory is living (in hours), # -1 means the directories are never deleted # Defaults is one week, i.e. 168 hours local.jobdir.maxlifespan=168 # Frequency of cleaning job directory (in minutes) # normal rate: once a date = 24 * 60 = 1440 -local.jobdir.cleaning.frequency=1 +local.jobdir.cleaning.frequency=1440 diff --git a/dundee-conf/Executable.properties b/dundee-conf/Executable.properties index a895f64..0ea7ed3 100644 --- a/dundee-conf/Executable.properties +++ b/dundee-conf/Executable.properties @@ -1,133 +1,257 @@ +########################################################################################### +# # +# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE FOR DUNDEE # +# # +########################################################################################### -### Clustal configuration ### -local.clustalw.bin.windows=binaries/windows/clustalw2.exe -local.clustalw.bin=binaries/src/clustalw/src/clustalw2 -cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2 -# Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison! -# see engine.client.Util.getExecProperty() method for details -# So they are case insensitive. -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=-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=/homes/pvtroshin/workspace/jaba2/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 if run on the cluster. -## This parameter specifies the number of CPUs to use -clustalo.cluster.cpunum=4 -## This reserves a slot with CPUNUM on the cluster for the task -clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00 - - -### Muscle configuration ### -local.muscle.bin.windows=binaries/windows/muscle.exe -local.muscle.bin=binaries/src/muscle/muscle -# Beware version of muscle on the cluster older and does not support some -# of the newer version attributed thus, will not work with Muscle.java wrapper! -cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle -#The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored -# e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path! -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=-l h_cpu=24:00:00 -l ram=6000M - -### Mafft configuration ### -#local.mafft.bin.windows= -local.mafft.bin=binaries/src/mafft/scripts/mafft -cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft +### 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 W CONFIGURATION # +########################################################################################### +local.clustalw.bin.windows = binaries/windows/clustalw2.exe +local.clustalw.bin = binaries/src/clustalw/src/clustalw2 +cluster.clustalw.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/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 -q 64bit-pri.q -q c6100.q -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 = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M + + +########################################################################################### +# MUSCLE CONFIGURATION # +########################################################################################### +local.muscle.bin.windows = binaries/windows/muscle.exe +local.muscle.bin = binaries/src/muscle/muscle +cluster.muscle.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M + + +########################################################################################### +# MAFFT CONFIGURATION # +########################################################################################### +local.mafft.bin = binaries/src/mafft/scripts/mafft +cluster.mafft.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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; -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=-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=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee -#/sw/bin/t_coffee -# Sub matrix support does not work -#tcoffee.-matrix.path=binaries/matrices +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 -q 64bit-pri.q -q c6100.q -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 = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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.cluster.cpunum=4 -tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 - -### Probcons configuration ### -#local.probcons.bin.windows= -local.probcons.bin=binaries/src/probcons/probcons -cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons -#Probcons does not support matrix loading - unrecognised option reported! -probcons.parameters.file=conf/settings/ProbconsParameters.xml -probcons.limits.file=conf/settings/ProbconsLimits.xml -probcons.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M - -### Jronn configuration ### -local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe -local.jronn.bin=/sw/java/latest/bin/java -cluster.jronn.bin=/sw/java/latest/bin/java -jronn.jar.file=binaries/windows/jronn3.1.jar -# jronn.parameters.file=conf/settings/JronnParameters.xml -jronn.limits.file=conf/settings/JronnLimits.xml -#TODO jronn.jvm.options=-Xms32M -Xmx512M -jronn.cluster.cpunum=4 -jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00 - - -### Disembl configuration Tisean - Disembl dependancy ### -#local.disembl.bin.windows= -local.disembl.bin=binaries/src/disembl/DisEMBL.py -cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py -# disembl.parameters.file=conf/settings/DisemblParameters.xml -disembl.limits.file=conf/settings/DisemblLimits.xml -disembl.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M - -### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### -#local.disembl.bin.windows= -local.globplot.bin=binaries/src/globplot/GlobPlot.py -cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py -# Dundee only settings -globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 -# globplot.parameters.file=conf/settings/GlobPlotParameters.xml -globplot.limits.file=conf/settings/GlobPlotLimits.xml -globplot.cluster.settings=-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 -#iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred -# This path will be converted to absolute if relative. -iupred.bin.env=IUPred_PATH#binaries/src/iupred -cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred -iupred.parameters.file=conf/settings/IUPredParameters.xml -iupred.limits.file=conf/settings/IUPredLimits.xml -iupred.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M - -### AACon configuration ### -# This is just a path to the standard java executable -local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe -local.aacon.bin=/sw/java/latest/bin/java -cluster.aacon.bin=/sw/java/latest/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.cluster.cpunum=4 -aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00 +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 -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M + + +########################################################################################### +# PROBCONS CONFIGURATION # +########################################################################################### +local.probcons.bin = binaries/src/probcons/probcons +cluster.probcons.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 -q 64bit-pri.q -q c6100.q -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 = /homes/www-jws2/java/jdk/bin/java +cluster.jronn.bin = /homes/www-jws2/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 -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=6000M + + +########################################################################################### +# DISEMBL CONFIGURATION # +########################################################################################### +local.disembl.bin = binaries/src/disembl/DisEMBL.py +cluster.disembl.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/disembl/DisEMBL.py +disembl.limits.file = conf/settings/DisemblLimits.xml +disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M + + +########################################################################################### +# GLOBPLOT CONFIGURATION # +########################################################################################### +local.globplot.bin = binaries/src/globplot/GlobPlot.py +cluster.globplot.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/GlobPlot.py +globplot.bin.env = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/biopython-1.50 +globplot.limits.file = conf/settings/GlobPlotLimits.xml +globplot.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -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 = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/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 -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M + + +########################################################################################### +# AACON CONFIGURATION # +########################################################################################### +### This is just a path to the standard java executable +local.aacon.bin = /homes/www-jws2/java/jdk/bin/java +cluster.aacon.bin = /homes/www-jws2/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 -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=3400M + +########################################################################################### +# JPRED CONFIGURATION # +########################################################################################### +#local.jpred.bin = binaries/src/jpred/jpred.pl +#cluster.jpred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/jpred/jpred.pl +## These paths will be converted to absolute if relative. +#jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast +## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If +## you install the database to a different path chenge the variable here +#jpred.data.uniref.path = /homes/www-jpred/databases +## WARNING!!! +## Redefine jpred.data.uniref.name if you do undestand what the variable means +#jpred.data.uniref.name = cluster +#### This parameters specifies the directory where the matrices files are stored +#jpred.presets.file = conf/settings/JpredPresets.xml +#jpred.parameters.file = conf/settings/JpredParameters.xml +#jpred.limits.file = conf/settings/JpredLimits.xml +#jpred.cluster.cpunum = 4 +#jpred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -pe smp 4 -l h_cpu=24:00:00 -l ram=8000M + +########################################################################################### +# RNAALIFOLD CONFIGURATION # +########################################################################################### +local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe +local.rnaalifold.bin = binaries/src/ViennaRNA/Progs/RNAalifold +cluster.rnaalifold.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/ViennaRNA/Progs/RNAalifold +rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml +rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml +rnaalifold.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M + +########################################################################################### +# MSAProbs CONFIGURATION # +########################################################################################### +local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs +cluster.msaprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs +msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml +msaprobs.limits.file = conf/settings/MSAprobsLimits.xml +msaprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M + +########################################################################################### +# GLprobs CONFIGURATION # +########################################################################################### +local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs +cluster.glprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/GLProbs-1.0/glprobs +glprobs.parameters.file = conf/settings/GLprobsParameters.xml +glprobs.limits.file = conf/settings/GLprobsLimits.xml +glprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M diff --git a/dundee-conf/GA.properties b/dundee-conf/GA.properties new file mode 100644 index 0000000..45352f0 --- /dev/null +++ b/dundee-conf/GA.properties @@ -0,0 +1,18 @@ +# This file contains settings for Google Analytics (GA) Statistics Engine. +# Feel free to remove/delete this file if you do not want us to see that you +# use JABAWS. However, we would appreciate it greatly if you could leave it on. +# JABAWS usage statistics are collected for funding and reporting purposes, and +# no private information is collected. The data sent by JABAWS is as follows: +# 1) The IP address of the JABAWS server machine. +# 2) The name of the web service that was called. +# 3) A few details of the system such as java version, user language, color depth, screen +# resolution and character encoding. + +# All calls to GA are completed asynchronously and create very little +# overhead. Thus they do not influence the server response time or performance. + +# Values yes or true = enable GA, any other value will disable it +enable.ga=no +# If set to yes replaces your server name/IP address with 127.0.0.1 +anonymize.ip=no + -- 1.7.10.2