#################################################################################\r
# enable or disable engine true | false\r
# OPTIONAL defaults to false\r
-engine.cluster.enable=false\r
+engine.cluster.enable=true\r
\r
#################################################################################\r
# Directory to use for temporary files storage\r
# REQUIRED - cluster nodes must have access to this directory!\r
-# WARNING!!! An absolute path is required \r
+# WARNING!!! An absolute path is required\r
#\r
# Please note that statistic web application will only be able to generate links\r
-# to the job folders if this path is within JABA web application. \r
-# JABAWS statistic application just assume that the last name in the path is the \r
-# application folder in the root of JABAWS web application. \r
-cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout\r
+# to the job folders if this path is within JABA web application.\r
+# JABAWS statistic application just assume that the last name in the path is the\r
+# application folder in the root of JABAWS web application.\r
+#####cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout\r
+cluster.tmp.directory=/homes/www-jws2/cluster_jobsout220\r
\r
#################################################################################\r
-# Enable/disable cluster statistics collector \r
+# Enable/disable cluster statistics collector\r
cluster.stat.collector.enable=false\r
# Frequency of statistics collecting (in minutes)\r
# normal rate: once a date = 24 * 60 = 1440\r
\r
#################################################################################\r
# Maximum amount of time the job is considered running in hours\r
-# Optional defaults to 7 days (168h) \r
+# Optional defaults to 7 days (168h)\r
cluster.stat.maxruntime=24\r
\r
#################################################################################\r
-# Maximum amount of time the job directory is living (in hours), \r
+# Maximum amount of time the job directory is living (in hours),\r
# -1 means the directories are never deleted\r
# Defaults is one week, i.e. 168 hours\r
cluster.jobdir.maxlifespan=168\r
# Frequency of cleaning job directory (in minutes)\r
# normal rate: once a date = 24 * 60 = 1440\r
-cluster.jobdir.cleaning.frequency=1\r
+cluster.jobdir.cleaning.frequency=1440\r
#################################################################################\r
# enable or disable engine true | false\r
# OPTIONAL defaults to true\r
-engine.local.enable=true \r
+engine.local.enable=true\r
\r
#################################################################################\r
# Directory to use for temporary files storage\r
# OPTIONAL defaults to java temporary directory \r
# Relative path within the project will be converted in absolute at runtime\r
#local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout \r
-local.tmp.directory=jobsout \r
+###local.tmp.directory=jobsout\r
+local.tmp.directory=/homes/www-jws2/local_jobsout220\r
\r
#################################################################################\r
-# Number of threads for tasks execution (valid values between 1 and 2x cpu. \r
+# Number of threads for tasks execution (valid values between 1 and 2x cpu.\r
# Where x is a number of cores available in the system)\r
-# OPTIONAL defaults to the number of cores for core number <=4 and \r
+# OPTIONAL defaults to the number of cores for core number <=4 and\r
# number of cores-1 for greater core numbers\r
engine.local.thread.number=2\r
\r
\r
# Maximum amount of time the job is considered running in hours\r
# Optional defaults to 24 hours\r
-local.stat.maxruntime=6\r
+local.stat.maxruntime=24\r
\r
#################################################################################\r
-# Maximum amount of time the job directory is living (in hours), \r
+# Maximum amount of time the job directory is living (in hours),\r
# -1 means the directories are never deleted\r
# Defaults is one week, i.e. 168 hours\r
local.jobdir.maxlifespan=168\r
# Frequency of cleaning job directory (in minutes)\r
# normal rate: once a date = 24 * 60 = 1440\r
-local.jobdir.cleaning.frequency=1\r
+local.jobdir.cleaning.frequency=1440\r
###########################################################################################\r
\r
### Properties supported by executables.\r
-### <execname> is one of the available applications: \r
+### <execname> is one of the available applications:\r
### [clustalw, mafft, muscle, propcons, tcoffee, iupred, jronn, globplot, disembl, aacon, jpred]\r
\r
-### Path to the native executable on Windows must be either absolute, \r
+### Path to the native executable on Windows must be either absolute,\r
### or relative to JABAWS web application\r
# local.<execname>.bin.windows = binaries/windows/clustalw2.exe\r
\r
### must be either absolute, or relative to JABAWS web application\r
# local.<execname>.bin = binaries/src/clustalw/src/clustalw2\r
\r
-### Path to the native executable on the cluster (must be accessible from all \r
-### cluster nodes which will run JABAWS jobs). The path must be absolute. \r
+### Path to the native executable on the Cluster (must be accessible from all\r
+### Cluster nodes which will run JABAWS jobs). The path must be absolute.\r
# cluster.<execname>.bin = /home/jabaws/binaries/src/clustalw/src/clustalw2\r
\r
### At least one of the path to the native executable should be defined.\r
\r
-### If an application supports presets, the preset file can have either \r
-### absolute or relative to the JABAWS web application path to the file. \r
+### If an application supports presets, the preset file can have either\r
+### absolute or relative to the JABAWS web application path to the file.\r
### The file is optional.\r
# <execname>.presets.file = conf/settings/ClustalPresets.xml\r
\r
-### If an application supports parameters, the parameter file can have either \r
-### absolute or relative to the JABAWS web application path to the file. \r
+### If an application supports parameters, the parameter file can have either\r
+### absolute or relative to the JABAWS web application path to the file.\r
### The file is optional.\r
# <execname>.parameters.file = conf/settings/ClustalParameters.xml\r
\r
-## Application limits, absolute or relative to \r
+## Application limits, absolute or relative to\r
## the JABAWS web application path to the file. Optional.\r
-## Use this if you want to limit the size of the job to be accepted by a \r
-## Webservice. The limits files we use in Dundee are provided with JABAWS. \r
+## Use this if you want to limit the size of the job to be accepted by a\r
+## Webservice. The limits files we use in Dundee are provided with JABAWS.\r
# <execname>.limits.file=conf/settings/ClustalLimits.xml\r
\r
-## Flags passed to the cluster batch manager for the application. Optional.\r
-## This example sets a maximum execution time to 24 hours and maximum amount of \r
-## memory per task to 6Gb for SGE and OGE cluster batch managers.\r
-## Please note that all the examples of this parameter below are correct for \r
-## Sun Grid Engine or Open Grid Engine (untested) only! If you use a different \r
-## batch manager you would need to specify different flags. \r
+## Flags passed to the Cluster batch manager for the application. Optional.\r
+## This example sets a maximum execution time to 24 hours and maximum amount of\r
+## memory per task to 6Gb for SGE and OGE Cluster batch managers.\r
+## Please note that all the examples of this parameter below are correct for\r
+## Sun Grid Engine or Open Grid Engine (untested) only! If you use a different\r
+## batch manager you would need to specify different flags.\r
# <execname>.cluster.settings = -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
\r
-## Environmental variables required by native executables. Optional. \r
-## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2; \r
+## Environmental variables required by native executables. Optional.\r
+## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2;\r
# <execname>.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
\r
-## Parameter supported by the executable Jar files, such as jronn and aacon, \r
-## point to the location of the jar file. Also, local.<execname>.bin, \r
-## local.<execname>.bin.windows properties are optional for these, if not \r
-## provided they will be replaced to the java executable path from JAVA_HOME \r
-## environmental variable. \r
+## Parameter supported by the executable Jar files, such as jronn and aacon,\r
+## point to the location of the jar file. Also, local.<execname>.bin,\r
+## local.<execname>.bin.windows properties are optional for these, if not\r
+## provided they will be replaced to the java executable path from JAVA_HOME\r
+## environmental variable.\r
#<execname>.jar.file = binaries/windows/bj3.0.4p-jronn.jar\r
\r
-\r
-\r
-\r
###########################################################################################\r
# CLUSTAL W CONFIGURATION #\r
###########################################################################################\r
local.clustalw.bin.windows = binaries/windows/clustalw2.exe\r
local.clustalw.bin = binaries/src/clustalw/src/clustalw2\r
-#cluster.clustalw.bin =/home/jabaws/binaries/src/clustalw/src/clustalw2\r
-### This parameter specifies the directory where the matrices files are stored\r
+cluster.clustalw.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/clustalw/src/clustalw2\r
+### This parameters specifies the directory where the matrices files are stored\r
clustalw.-matrix.path = binaries/matrices\r
clustalw.presets.file = conf/settings/ClustalPresets.xml\r
clustalw.parameters.file = conf/settings/ClustalParameters.xml\r
-clustalw.limits.file = conf/settings/ClustalLimits.xml\r
-#clustalw.cluster.settings =-l h_cpu=24:00:00 -l ram=6000M\r
+clustalw.limits.file = conf/settings/ClustalLimits.xml\r
+clustalw.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
\r
\r
###########################################################################################\r
-# CLUSTAL OMEGA CONFIGURATION #\r
+# CLUSTAL OMEGA CONFIGURATION #\r
###########################################################################################\r
local.clustalo.bin.windows = binaries/windows/clustalo/clustalo.exe\r
local.clustalo.bin = binaries/src/clustalo/src/clustalo\r
-#cluster.clustalo.bin = /home/jabaws/binaries/src/clustalo/src/clustalo\r
-### This parameter specifies the directory where the matrices files are stored\r
+cluster.clustalo.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/clustalo/src/clustalo\r
+### This parameters specifies the directory where the matrices files are stored\r
#clustalo.presets.file = conf/settings/ClustaloPresets.xml\r
clustalo.parameters.file = conf/settings/ClustaloParameters.xml\r
clustalo.limits.file = conf/settings/ClustaloLimits.xml\r
-### ClustalO can be run on multiple CPUs on the cluster. This parameter specifies CPU #NN\r
+### ClustalO can be executed on multiple CPUs. This parameter specifies the number of CPUs:\r
clustalo.cluster.cpunum = 4\r
-### This reserves a slot with CPUNUM on the cluster for the task\r
-#clustalo.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00\r
+### This reserves a slot with CPUNUM on the Cluster for the task\r
+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\r
\r
\r
###########################################################################################\r
-# MUSCLE CONFIGURATION #\r
+# MUSCLE CONFIGURATION #\r
###########################################################################################\r
local.muscle.bin.windows = binaries/windows/muscle.exe\r
local.muscle.bin = binaries/src/muscle/muscle\r
-#cluster.muscle.bin = /home/jabaws/binaries/src/muscle/muscle\r
-### This parameter specifies the directory where the matrices files are stored\r
+cluster.muscle.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/muscle/muscle\r
+### This parameters specifies the directory where the matrices files are stored\r
muscle.-matrix.path = binaries/matrices\r
muscle.presets.file = conf/settings/MusclePresets.xml\r
muscle.parameters.file = conf/settings/MuscleParameters.xml\r
muscle.limits.file = conf/settings/MuscleLimits.xml\r
-#muscle.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+muscle.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
\r
\r
###########################################################################################\r
-# MAFFT CONFIGURATION #\r
+# MAFFT CONFIGURATION #\r
###########################################################################################\r
-local.mafft.bin = binaries/src/mafft/scripts/mafft\r
-#cluster.mafft.bin = /home/jabaws/binaries/src/mafft/scripts/mafft\r
+local.mafft.bin = binaries/src/mafft/scripts/mafft\r
+cluster.mafft.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/mafft/scripts/mafft\r
# These paths will be converted to absolute if relative.\r
-mafft.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
+mafft.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
### This parameters specifies the directory where the matrices files are stored\r
-mafft.--aamatrix.path = binaries/matrices\r
-mafft.presets.file = conf/settings/MafftPresets.xml\r
-mafft.parameters.file = conf/settings/MafftParameters.xml\r
-mafft.limits.file = conf/settings/MafftLimits.xml\r
-#mafft.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+mafft.--aamatrix.path = binaries/matrices\r
+mafft.presets.file = conf/settings/MafftPresets.xml\r
+mafft.parameters.file = conf/settings/MafftParameters.xml\r
+mafft.limits.file = conf/settings/MafftLimits.xml\r
+mafft.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
\r
\r
###########################################################################################\r
-# TCOFFEE CONFIGURATION #\r
+# TCOFFEE CONFIGURATION #\r
###########################################################################################\r
-local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee\r
-#cluster.tcoffee.bin = /home/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee\r
+local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee\r
+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\r
# This variable is required by tcoffee\r
-tcoffee.bin.env = HOME_4_TCOFFEE#jobsout;\r
-tcoffee.presets.file = conf/settings/TcoffeePresets.xml\r
-tcoffee.parameters.file = conf/settings/TcoffeeParameters.xml\r
-tcoffee.limits.file = conf/settings/TcoffeeLimits.xml\r
-### Tcoffee can be executed on multiple CPUs if run on the cluster. This parameter defines CPUs #N\r
-#tcoffee.cluster.cpunum = 4\r
-### This paramer defines queue setting with CPUNUM on the cluster\r
-#tcoffee.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00\r
+tcoffee.bin.env = HOME_4_TCOFFEE#jobsout;\r
+tcoffee.presets.file = conf/settings/TcoffeePresets.xml\r
+tcoffee.parameters.file = conf/settings/TcoffeeParameters.xml\r
+tcoffee.limits.file = conf/settings/TcoffeeLimits.xml\r
+### Tcoffee can be executed on multiple CPUs. This parameter specifies the number of CPUs:\r
+tcoffee.cluster.cpunum = 4\r
+### This reserves a slot with CPUNUM on the Cluster for the task\r
+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\r
\r
\r
###########################################################################################\r
-# PROBCONS CONFIGURATION #\r
+# PROBCONS CONFIGURATION #\r
###########################################################################################\r
local.probcons.bin = binaries/src/probcons/probcons\r
-#cluster.probcons.bin = /home/jabaws/binaries/src/probcons/probcons\r
+cluster.probcons.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/probcons/probcons\r
probcons.parameters.file = conf/settings/ProbconsParameters.xml\r
probcons.limits.file = conf/settings/ProbconsLimits.xml\r
-### This parameter defines queue settings for PROBCON on the cluster\r
-#probcons.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+probcons.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
\r
\r
###########################################################################################\r
-# JRONN CONFIGURATION #\r
+# JRONN CONFIGURATION #\r
###########################################################################################\r
-### If no local path is specified, Java is loaded from JAVA_HOME variable for local \r
-### execution. However, cluster.jronn.bin MUST be specified for running Jronn on the cluster.\r
-#local.jronn.bin.windows = D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
-#local.jronn.bin = /sw/java/latest/bin/java\r
-#cluster.jronn.bin = /sw/java/latest/bin/java\r
+### If no local path is specified, Java is loaded from JAVA_HOME variable for local execution\r
+### However, cluster.jronn.bin MUST be specified for running Jronn on the Cluster.\r
+#local.jronn.bin.windows = D:\\Java\\jdk1.6.0_24\\bin\\java.exe\r
+local.jronn.bin = /homes/www-jws2/java/jdk/bin/java\r
+cluster.jronn.bin = /homes/www-jws2/java/jdk/bin/java\r
jronn.jar.file = binaries/windows/bj3.0.4p-jronn.jar\r
jronn.limits.file = conf/settings/JronnLimits.xml\r
-## Jronn can use multiple CPUs. This parameter specifies the number of CPUs\r
-#jronn.cluster.cpunum = 4\r
-### This reserves a slot with CPUNUM on the cluster for the task\r
-#jronn.cluster.settings = -q 64bit-pri.q -pe smp 4 -l h_cpu=24:00:00\r
+### Jronn can use multiple CPUs. This parameter specifies the number of CPU:\r
+jronn.cluster.cpunum = 4\r
+### This reserves a slot with CPUNUM on the Cluster for the task\r
+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\r
\r
\r
###########################################################################################\r
-# DISEMBL CONFIGURATION #\r
+# DISEMBL CONFIGURATION #\r
###########################################################################################\r
-local.disembl.bin = binaries/src/disembl/DisEMBL.py\r
-#cluster.disembl.bin = /home/jabaws/binaries/src/disembl/DisEMBL.py\r
-disembl.limits.file = conf/settings/DisemblLimits.xml\r
-#disembl.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+local.disembl.bin = binaries/src/disembl/DisEMBL.py\r
+cluster.disembl.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/disembl/DisEMBL.py\r
+disembl.limits.file = conf/settings/DisemblLimits.xml\r
+disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
\r
\r
###########################################################################################\r
-# GLOBPLOT CONFIGURATION #\r
+# GLOBPLOT CONFIGURATION #\r
###########################################################################################\r
-local.globplot.bin = binaries/src/globplot/GlobPlot.py\r
-#cluster.globplot.bin = /home/jabaws/binaries/src/globplot/GlobPlot.py\r
-#globplot.bin.env = PYTHONPATH#/home/jabaws/binaries/src/globplot/biopython-1.50\r
-globplot.limits.file = conf/settings/GlobPlotLimits.xml\r
-#globplot.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+local.globplot.bin = binaries/src/globplot/GlobPlot.py\r
+cluster.globplot.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/GlobPlot.py\r
+globplot.bin.env = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/biopython-1.50\r
+globplot.limits.file = conf/settings/GlobPlotLimits.xml\r
+globplot.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
\r
\r
###########################################################################################\r
-# IUPRED CONFIGURATION #\r
+# IUPRED CONFIGURATION #\r
###########################################################################################\r
-local.iupred.bin.windows = binaries/windows/iupred/iupred.exe \r
+#local.iupred.bin.windows = binaries/windows/iupred/iupred.exe\r
local.iupred.bin = binaries/src/iupred/iupred\r
-### This must point to the directory where iupred binary is, with other files it \r
-### depends on. This path will be converted to absolute if relative at runtime. \r
+### This must point to the directory where iupred binary is, with other files it\r
+### depends on. This path will be converted to absolute if relative at runtime.\r
iupred.bin.env = IUPred_PATH#binaries/src/iupred\r
-#cluster.iupred.bin = /home/jabaws/binaries/src/iupred/iupred\r
+cluster.iupred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/iupred/iupred\r
iupred.parameters.file = conf/settings/IUPredParameters.xml\r
iupred.limits.file = conf/settings/IUPredLimits.xml\r
-#iupred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+iupred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
\r
\r
###########################################################################################\r
-# AACON CONFIGURATION #\r
+# AACON CONFIGURATION #\r
###########################################################################################\r
-### This is just a path to the standard java executable \r
-#local.aacon.bin.windows = D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
-#local.aacon.bin = /sw/java/latest/bin/java\r
-#cluster.aacon.bin = /sw/java/latest/bin/java\r
+### This is just a path to the standard java executable\r
+local.aacon.bin = /homes/www-jws2/java/jdk/bin/java\r
+cluster.aacon.bin = /homes/www-jws2/java/jdk/bin/java\r
### Path to the AACon library\r
aacon.jar.file = binaries/windows/aaconservation.jar\r
aacon.parameters.file = conf/settings/AAConParameters.xml\r
aacon.presets.file = conf/settings/AAConPresets.xml\r
aacon.limits.file = conf/settings/AAConLimits.xml\r
-### AACon can use multiple CPUs. This parameter defines the number of CPUs:\r
-#aacon.cluster.cpunum = 4\r
-### This parameter defines queue settings for AACON on the cluster\r
-#aacon.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00\r
+### AACon can use multiple CPUs\r
+### This parameter specifies the number of CPUs to use\r
+aacon.cluster.cpunum = 4\r
+### This reserves a slot with CPUNUM on the Cluster for the task\r
+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\r
\r
###########################################################################################\r
# JPRED CONFIGURATION #\r
###########################################################################################\r
#local.jpred.bin = binaries/src/jpred/jpred.pl\r
-##cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl\r
+#cluster.jpred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/jpred/jpred.pl\r
## These paths will be converted to absolute if relative.\r
#jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast\r
## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If\r
## you install the database to a different path chenge the variable here\r
-#jpred.data.uniref.path = /data/UNIREFdb\r
+#jpred.data.uniref.path = /homes/www-jpred/databases\r
## WARNING!!!\r
## Redefine jpred.data.uniref.name if you do undestand what the variable means\r
#jpred.data.uniref.name = cluster\r
#jpred.parameters.file = conf/settings/JpredParameters.xml\r
#jpred.limits.file = conf/settings/JpredLimits.xml\r
#jpred.cluster.cpunum = 4\r
-##jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
+#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\r
\r
###########################################################################################\r
# RNAALIFOLD CONFIGURATION #\r
###########################################################################################\r
local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe\r
local.rnaalifold.bin = binaries/src/ViennaRNA/Progs/RNAalifold\r
-#cluster.rnaalifold.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/ViennaRNA/Progs/RNAalifold\r
+cluster.rnaalifold.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/ViennaRNA/Progs/RNAalifold\r
rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml\r
rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml\r
-#rnaalifold.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r
+rnaalifold.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
\r
###########################################################################################\r
# MSAProbs CONFIGURATION #\r
###########################################################################################\r
local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs\r
-#cluster.msaprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs\r
+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\r
msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml\r
msaprobs.limits.file = conf/settings/MSAprobsLimits.xml\r
-#msaprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r
+msaprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
\r
###########################################################################################\r
# GLprobs CONFIGURATION #\r
###########################################################################################\r
local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs\r
-#cluster.glprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/GLProbs-1.0/glprobs\r
+cluster.glprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/GLProbs-1.0/glprobs\r
glprobs.parameters.file = conf/settings/GLprobsParameters.xml\r
glprobs.limits.file = conf/settings/GLprobsLimits.xml\r
-#glprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r
+glprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
###########################################################################################
# #
-# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE #
+# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE FOR DUNDEE #
# #
###########################################################################################
### Properties supported by executables.
-### <execname> is one of the available applications:
+### <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,
+### 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
### 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.
+### 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.
+### 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.
+### 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
+## 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.
# <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.
+## 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;
+## 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.
+## 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 #
+# 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
###########################################################################################
###########################################################################################
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
###########################################################################################
###########################################################################################
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
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
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
### 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
#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
#################################################################################\r
# Directory to use for temporary files storage\r
# REQUIRED - cluster nodes must have access to this directory!\r
-# WARNING!!! An absolute path is required \r
+# WARNING!!! An absolute path is required\r
#\r
# Please note that statistic web application will only be able to generate links\r
-# to the job folders if this path is within JABA web application. \r
-# JABAWS statistic application just assume that the last name in the path is the \r
-# application folder in the root of JABAWS web application. \r
-cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout\r
+# to the job folders if this path is within JABA web application.\r
+# JABAWS statistic application just assume that the last name in the path is the\r
+# application folder in the root of JABAWS web application.\r
+#####cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout\r
+cluster.tmp.directory=/homes/www-jws2/cluster_jobsout220\r
\r
#################################################################################\r
-# Enable/disable cluster statistics collector \r
-cluster.stat.collector.enable=true\r
+# Enable/disable cluster statistics collector\r
+cluster.stat.collector.enable=false\r
# Frequency of statistics collecting (in minutes)\r
# normal rate: once a date = 24 * 60 = 1440\r
cluster.stat.collector.update.frequency=1440\r
\r
#################################################################################\r
# Maximum amount of time the job is considered running in hours\r
-# Optional defaults to 7 days (168h) \r
+# Optional defaults to 7 days (168h)\r
cluster.stat.maxruntime=24\r
\r
#################################################################################\r
-# Maximum amount of time the job directory is living (in hours), \r
+# Maximum amount of time the job directory is living (in hours),\r
# -1 means the directories are never deleted\r
# Defaults is one week, i.e. 168 hours\r
cluster.jobdir.maxlifespan=168\r
# Frequency of cleaning job directory (in minutes)\r
# normal rate: once a date = 24 * 60 = 1440\r
-cluster.jobdir.cleaning.frequency=1\r
+cluster.jobdir.cleaning.frequency=1440\r
#################################################################################\r
# enable or disable engine true | false\r
# OPTIONAL defaults to true\r
-engine.local.enable=true \r
+engine.local.enable=true\r
\r
#################################################################################\r
# Directory to use for temporary files storage\r
# OPTIONAL defaults to java temporary directory \r
# Relative path within the project will be converted in absolute at runtime\r
-local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout \r
-#local.tmp.directory=jobsout \r
+#local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout\r
+###local.tmp.directory=jobsout\r
+local.tmp.directory=/homes/www-jws2/local_jobsout220\r
\r
#################################################################################\r
-# Number of threads for tasks execution (valid values between 1 and 2x cpu. \r
+# Number of threads for tasks execution (valid values between 1 and 2x cpu.\r
# Where x is a number of cores available in the system)\r
-# OPTIONAL defaults to the number of cores for core number <=4 and \r
+# OPTIONAL defaults to the number of cores for core number <=4 and\r
# number of cores-1 for greater core numbers\r
engine.local.thread.number=2\r
\r
\r
# Maximum amount of time the job is considered running in hours\r
# Optional defaults to 24 hours\r
-local.stat.maxruntime=6\r
+local.stat.maxruntime=24\r
\r
#################################################################################\r
-# Maximum amount of time the job directory is living (in hours), \r
+# Maximum amount of time the job directory is living (in hours),\r
# -1 means the directories are never deleted\r
# Defaults is one week, i.e. 168 hours\r
local.jobdir.maxlifespan=168\r
# Frequency of cleaning job directory (in minutes)\r
# normal rate: once a date = 24 * 60 = 1440\r
-local.jobdir.cleaning.frequency=1\r
+local.jobdir.cleaning.frequency=1440\r
+###########################################################################################\r
+# #\r
+# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE FOR DUNDEE #\r
+# #\r
+###########################################################################################\r
\r
-### Clustal configuration ###\r
-local.clustalw.bin.windows=binaries/windows/clustalw2.exe\r
-local.clustalw.bin=binaries/src/clustalw/src/clustalw2\r
-cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2\r
-# Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!\r
-# see engine.client.Util.getExecProperty() method for details \r
-# So they are case insensitive. \r
-clustalw.-matrix.path=binaries/matrices\r
-clustalw.presets.file=conf/settings/ClustalPresets.xml\r
-clustalw.parameters.file=conf/settings/ClustalParameters.xml\r
-clustalw.limits.file=conf/settings/ClustalLimits.xml\r
-clustalw.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
-\r
-###### CLUSTAL OMEGA CONFIGURATION ######\r
-local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe\r
-local.clustalo.bin=binaries/src/clustalo/src/clustalo\r
-cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo\r
-## This parameters specifies the directory where the matrices files are stored \r
-#clustalo.presets.file=conf/settings/ClustaloPresets.xml\r
-clustalo.parameters.file=conf/settings/ClustaloParameters.xml\r
-clustalo.limits.file=conf/settings/ClustaloLimits.xml\r
-## ClustalO can be executed on multiple CPUs if run on the cluster. \r
-## This parameter specifies the number of CPUs to use\r
-clustalo.cluster.cpunum=4\r
-## This reserves a slot with CPUNUM on the cluster for the task\r
-clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00 \r
-\r
-\r
-### Muscle configuration ###\r
-local.muscle.bin.windows=binaries/windows/muscle.exe\r
-local.muscle.bin=binaries/src/muscle/muscle\r
-# Beware version of muscle on the cluster older and does not support some \r
-# of the newer version attributed thus, will not work with Muscle.java wrapper!\r
-cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle\r
-#The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored\r
-# e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!\r
-muscle.-matrix.path=binaries/matrices\r
-muscle.presets.file=conf/settings/MusclePresets.xml\r
-muscle.parameters.file=conf/settings/MuscleParameters.xml\r
-muscle.limits.file=conf/settings/MuscleLimits.xml\r
-muscle.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
-\r
-### Mafft configuration ###\r
-#local.mafft.bin.windows=\r
-local.mafft.bin=binaries/src/mafft/scripts/mafft\r
-cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft\r
+### Properties supported by executables.\r
+### <execname> is one of the available applications:\r
+### [clustalw, mafft, muscle, propcons, tcoffee, iupred, jronn, globplot, disembl, aacon, jpred]\r
+\r
+### Path to the native executable on Windows must be either absolute,\r
+### or relative to JABAWS web application\r
+# local.<execname>.bin.windows = binaries/windows/clustalw2.exe\r
+\r
+### Path to the native executable not on Windows (e.g. Linux, Mac)\r
+### must be either absolute, or relative to JABAWS web application\r
+# local.<execname>.bin = binaries/src/clustalw/src/clustalw2\r
+\r
+### Path to the native executable on the Cluster (must be accessible from all\r
+### Cluster nodes which will run JABAWS jobs). The path must be absolute.\r
+# cluster.<execname>.bin = /home/jabaws/binaries/src/clustalw/src/clustalw2\r
+\r
+### At least one of the path to the native executable should be defined.\r
+\r
+### If an application supports presets, the preset file can have either\r
+### absolute or relative to the JABAWS web application path to the file.\r
+### The file is optional.\r
+# <execname>.presets.file = conf/settings/ClustalPresets.xml\r
+\r
+### If an application supports parameters, the parameter file can have either\r
+### absolute or relative to the JABAWS web application path to the file.\r
+### The file is optional.\r
+# <execname>.parameters.file = conf/settings/ClustalParameters.xml\r
+\r
+## Application limits, absolute or relative to\r
+## the JABAWS web application path to the file. Optional.\r
+## Use this if you want to limit the size of the job to be accepted by a\r
+## Webservice. The limits files we use in Dundee are provided with JABAWS.\r
+# <execname>.limits.file=conf/settings/ClustalLimits.xml\r
+\r
+## Flags passed to the Cluster batch manager for the application. Optional.\r
+## This example sets a maximum execution time to 24 hours and maximum amount of\r
+## memory per task to 6Gb for SGE and OGE Cluster batch managers.\r
+## Please note that all the examples of this parameter below are correct for\r
+## Sun Grid Engine or Open Grid Engine (untested) only! If you use a different\r
+## batch manager you would need to specify different flags.\r
+# <execname>.cluster.settings = -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+## Environmental variables required by native executables. Optional.\r
+## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2;\r
+# <execname>.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
+\r
+## Parameter supported by the executable Jar files, such as jronn and aacon,\r
+## point to the location of the jar file. Also, local.<execname>.bin,\r
+## local.<execname>.bin.windows properties are optional for these, if not\r
+## provided they will be replaced to the java executable path from JAVA_HOME\r
+## environmental variable.\r
+#<execname>.jar.file = binaries/windows/bj3.0.4p-jronn.jar\r
+\r
+###########################################################################################\r
+# CLUSTAL W CONFIGURATION #\r
+###########################################################################################\r
+local.clustalw.bin.windows = binaries/windows/clustalw2.exe\r
+local.clustalw.bin = binaries/src/clustalw/src/clustalw2\r
+cluster.clustalw.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/clustalw/src/clustalw2\r
+### This parameters specifies the directory where the matrices files are stored\r
+clustalw.-matrix.path = binaries/matrices\r
+clustalw.presets.file = conf/settings/ClustalPresets.xml\r
+clustalw.parameters.file = conf/settings/ClustalParameters.xml\r
+clustalw.limits.file = conf/settings/ClustalLimits.xml\r
+clustalw.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# CLUSTAL OMEGA CONFIGURATION #\r
+###########################################################################################\r
+local.clustalo.bin.windows = binaries/windows/clustalo/clustalo.exe\r
+local.clustalo.bin = binaries/src/clustalo/src/clustalo\r
+cluster.clustalo.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/clustalo/src/clustalo\r
+### This parameters specifies the directory where the matrices files are stored\r
+#clustalo.presets.file = conf/settings/ClustaloPresets.xml\r
+clustalo.parameters.file = conf/settings/ClustaloParameters.xml\r
+clustalo.limits.file = conf/settings/ClustaloLimits.xml\r
+### ClustalO can be executed on multiple CPUs. This parameter specifies the number of CPUs:\r
+clustalo.cluster.cpunum = 4\r
+### This reserves a slot with CPUNUM on the Cluster for the task\r
+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\r
+\r
+\r
+###########################################################################################\r
+# MUSCLE CONFIGURATION #\r
+###########################################################################################\r
+local.muscle.bin.windows = binaries/windows/muscle.exe\r
+local.muscle.bin = binaries/src/muscle/muscle\r
+cluster.muscle.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/muscle/muscle\r
+### This parameters specifies the directory where the matrices files are stored\r
+muscle.-matrix.path = binaries/matrices\r
+muscle.presets.file = conf/settings/MusclePresets.xml\r
+muscle.parameters.file = conf/settings/MuscleParameters.xml\r
+muscle.limits.file = conf/settings/MuscleLimits.xml\r
+muscle.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# MAFFT CONFIGURATION #\r
+###########################################################################################\r
+local.mafft.bin = binaries/src/mafft/scripts/mafft\r
+cluster.mafft.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/mafft/scripts/mafft\r
# These paths will be converted to absolute if relative.\r
-mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
-mafft.--aamatrix.path=binaries/matrices\r
-mafft.presets.file=conf/settings/MafftPresets.xml\r
-mafft.parameters.file=conf/settings/MafftParameters.xml\r
-mafft.limits.file=conf/settings/MafftLimits.xml\r
-mafft.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
-\r
-\r
-### Tcoffee configuration ###\r
-local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee\r
-cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
-#/sw/bin/t_coffee\r
-# Sub matrix support does not work \r
-#tcoffee.-matrix.path=binaries/matrices\r
+mafft.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
+### This parameters specifies the directory where the matrices files are stored\r
+mafft.--aamatrix.path = binaries/matrices\r
+mafft.presets.file = conf/settings/MafftPresets.xml\r
+mafft.parameters.file = conf/settings/MafftParameters.xml\r
+mafft.limits.file = conf/settings/MafftLimits.xml\r
+mafft.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# TCOFFEE CONFIGURATION #\r
+###########################################################################################\r
+local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee\r
+cluster.tcoffee.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/tcoffee/t_coffee_source/t_coffee\r
# This variable is required by tcoffee\r
-tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;\r
-tcoffee.presets.file=conf/settings/TcoffeePresets.xml\r
-tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml\r
-tcoffee.limits.file=conf/settings/TcoffeeLimits.xml\r
-tcoffee.cluster.cpunum=4\r
-tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 \r
-\r
-### Probcons configuration ###\r
-#local.probcons.bin.windows=\r
-local.probcons.bin=binaries/src/probcons/probcons\r
-cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons\r
-#Probcons does not support matrix loading - unrecognised option reported! \r
-probcons.parameters.file=conf/settings/ProbconsParameters.xml\r
-probcons.limits.file=conf/settings/ProbconsLimits.xml\r
-probcons.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
-\r
-### Jronn configuration ### \r
-local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
-local.jronn.bin=/sw/java/latest/bin/java\r
-cluster.jronn.bin=/sw/java/latest/bin/java\r
-jronn.jar.file=binaries/windows/jronn3.1.jar\r
-# jronn.parameters.file=conf/settings/JronnParameters.xml\r
-jronn.limits.file=conf/settings/JronnLimits.xml\r
-#TODO jronn.jvm.options=-Xms32M -Xmx512M\r
-jronn.cluster.cpunum=4\r
-jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00\r
-\r
-\r
-### Disembl configuration Tisean - Disembl dependancy ### \r
-#local.disembl.bin.windows= \r
-local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
-cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
-# disembl.parameters.file=conf/settings/DisemblParameters.xml\r
-disembl.limits.file=conf/settings/DisemblLimits.xml\r
-disembl.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
-\r
-### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### \r
-#local.disembl.bin.windows= \r
-local.globplot.bin=binaries/src/globplot/GlobPlot.py\r
-cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
-# Dundee only settings\r
-globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 \r
-# globplot.parameters.file=conf/settings/GlobPlotParameters.xml\r
-globplot.limits.file=conf/settings/GlobPlotLimits.xml\r
-globplot.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
-\r
-### IUPred configuration ### \r
-local.iupred.bin.windows=binaries/windows/iupred/iupred.exe \r
-local.iupred.bin=binaries/src/iupred/iupred\r
-# This must point to the directory where iupred binary is, with other files it depends on\r
-#iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred\r
-# This path will be converted to absolute if relative. \r
-iupred.bin.env=IUPred_PATH#binaries/src/iupred\r
-cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred\r
-iupred.parameters.file=conf/settings/IUPredParameters.xml\r
-iupred.limits.file=conf/settings/IUPredLimits.xml\r
-iupred.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
-\r
-### AACon configuration ###\r
-# This is just a path to the standard java executable \r
-local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
-local.aacon.bin=/sw/java/latest/bin/java\r
-cluster.aacon.bin=/sw/java/latest/bin/java\r
-# Path to the AACon library\r
-aacon.jar.file=binaries/windows/aaconservation.jar\r
-aacon.parameters.file=conf/settings/AAConParameters.xml\r
-aacon.presets.file=conf/settings/AAConPresets.xml\r
-aacon.limits.file=conf/settings/AAConLimits.xml\r
-aacon.cluster.cpunum=4\r
-aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00\r
+tcoffee.bin.env = HOME_4_TCOFFEE#jobsout;\r
+tcoffee.presets.file = conf/settings/TcoffeePresets.xml\r
+tcoffee.parameters.file = conf/settings/TcoffeeParameters.xml\r
+tcoffee.limits.file = conf/settings/TcoffeeLimits.xml\r
+### Tcoffee can be executed on multiple CPUs. This parameter specifies the number of CPUs:\r
+tcoffee.cluster.cpunum = 4\r
+### This reserves a slot with CPUNUM on the Cluster for the task\r
+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\r
+\r
+\r
+###########################################################################################\r
+# PROBCONS CONFIGURATION #\r
+###########################################################################################\r
+local.probcons.bin = binaries/src/probcons/probcons\r
+cluster.probcons.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/probcons/probcons\r
+probcons.parameters.file = conf/settings/ProbconsParameters.xml\r
+probcons.limits.file = conf/settings/ProbconsLimits.xml\r
+probcons.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# JRONN CONFIGURATION #\r
+###########################################################################################\r
+### If no local path is specified, Java is loaded from JAVA_HOME variable for local execution\r
+### However, cluster.jronn.bin MUST be specified for running Jronn on the Cluster.\r
+#local.jronn.bin.windows = D:\\Java\\jdk1.6.0_24\\bin\\java.exe\r
+local.jronn.bin = /homes/www-jws2/java/jdk/bin/java\r
+cluster.jronn.bin = /homes/www-jws2/java/jdk/bin/java\r
+jronn.jar.file = binaries/windows/bj3.0.4p-jronn.jar\r
+jronn.limits.file = conf/settings/JronnLimits.xml\r
+### Jronn can use multiple CPUs. This parameter specifies the number of CPU:\r
+jronn.cluster.cpunum = 4\r
+### This reserves a slot with CPUNUM on the Cluster for the task\r
+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\r
+\r
+\r
+###########################################################################################\r
+# DISEMBL CONFIGURATION #\r
+###########################################################################################\r
+local.disembl.bin = binaries/src/disembl/DisEMBL.py\r
+cluster.disembl.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/disembl/DisEMBL.py\r
+disembl.limits.file = conf/settings/DisemblLimits.xml\r
+disembl.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# GLOBPLOT CONFIGURATION #\r
+###########################################################################################\r
+local.globplot.bin = binaries/src/globplot/GlobPlot.py\r
+cluster.globplot.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/GlobPlot.py\r
+globplot.bin.env = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/globplot/biopython-1.50\r
+globplot.limits.file = conf/settings/GlobPlotLimits.xml\r
+globplot.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# IUPRED CONFIGURATION #\r
+###########################################################################################\r
+#local.iupred.bin.windows = binaries/windows/iupred/iupred.exe\r
+local.iupred.bin = binaries/src/iupred/iupred\r
+### This must point to the directory where iupred binary is, with other files it\r
+### depends on. This path will be converted to absolute if relative at runtime.\r
+iupred.bin.env = IUPred_PATH#binaries/src/iupred\r
+cluster.iupred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/iupred/iupred\r
+iupred.parameters.file = conf/settings/IUPredParameters.xml\r
+iupred.limits.file = conf/settings/IUPredLimits.xml\r
+iupred.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+\r
+###########################################################################################\r
+# AACON CONFIGURATION #\r
+###########################################################################################\r
+### This is just a path to the standard java executable\r
+local.aacon.bin = /homes/www-jws2/java/jdk/bin/java\r
+cluster.aacon.bin = /homes/www-jws2/java/jdk/bin/java\r
+### Path to the AACon library\r
+aacon.jar.file = binaries/windows/aaconservation.jar\r
+aacon.parameters.file = conf/settings/AAConParameters.xml\r
+aacon.presets.file = conf/settings/AAConPresets.xml\r
+aacon.limits.file = conf/settings/AAConLimits.xml\r
+### AACon can use multiple CPUs\r
+### This parameter specifies the number of CPUs to use\r
+aacon.cluster.cpunum = 4\r
+### This reserves a slot with CPUNUM on the Cluster for the task\r
+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\r
+\r
+###########################################################################################\r
+# JPRED CONFIGURATION #\r
+###########################################################################################\r
+#local.jpred.bin = binaries/src/jpred/jpred.pl\r
+#cluster.jpred.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/jpred/jpred.pl\r
+## These paths will be converted to absolute if relative.\r
+#jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast\r
+## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If\r
+## you install the database to a different path chenge the variable here\r
+#jpred.data.uniref.path = /homes/www-jpred/databases\r
+## WARNING!!!\r
+## Redefine jpred.data.uniref.name if you do undestand what the variable means\r
+#jpred.data.uniref.name = cluster\r
+#### This parameters specifies the directory where the matrices files are stored\r
+#jpred.presets.file = conf/settings/JpredPresets.xml\r
+#jpred.parameters.file = conf/settings/JpredParameters.xml\r
+#jpred.limits.file = conf/settings/JpredLimits.xml\r
+#jpred.cluster.cpunum = 4\r
+#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\r
+\r
+###########################################################################################\r
+# RNAALIFOLD CONFIGURATION #\r
+###########################################################################################\r
+local.rnaalifold.bin.windows = binaries/windows/ViennaRNA/RNAalifold.exe\r
+local.rnaalifold.bin = binaries/src/ViennaRNA/Progs/RNAalifold\r
+cluster.rnaalifold.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/ViennaRNA/Progs/RNAalifold\r
+rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml\r
+rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml\r
+rnaalifold.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+###########################################################################################\r
+# MSAProbs CONFIGURATION #\r
+###########################################################################################\r
+local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs\r
+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\r
+msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml\r
+msaprobs.limits.file = conf/settings/MSAprobsLimits.xml\r
+msaprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
+\r
+###########################################################################################\r
+# GLprobs CONFIGURATION #\r
+###########################################################################################\r
+local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs\r
+cluster.glprobs.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws-dev/binaries/src/GLProbs-1.0/glprobs\r
+glprobs.parameters.file = conf/settings/GLprobsParameters.xml\r
+glprobs.limits.file = conf/settings/GLprobsLimits.xml\r
+glprobs.cluster.settings = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu=24:00:00 -l ram=6000M\r
--- /dev/null
+# 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
+
git://source.jalview.org / jabaws.git / commitdiff