###########################################################################################
# #
-# 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/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/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/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
+local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee.sh
+cluster.tcoffee.bin = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee.sh
# 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/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/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/binaries/src/globplot/GlobPlot.py
+globplot.bin.env = PYTHONPATH#/homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/globplot/biopython-1.50
globplot.limits.file = conf/settings/GlobPlotLimits.xml
-globplot.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M
+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/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.jar.file = binaries/windows/compbio-conservation-1.1.jar
aacon.parameters.file = conf/settings/AAConParameters.xml
aacon.presets.file = conf/settings/AAConPresets.xml
aacon.limits.file = conf/settings/AAConLimits.xml
### AACon can use multiple CPUs
### This parameter specifies the number of CPUs to use
aacon.cluster.cpunum = 4
-### This reserves a slot with CPUNUM on the cluster for the task
-aacon.cluster.settings = -P webservices -R y -q 64bit-pri.q -pe smp 4 -l ram=3400M -l h_cpu=24:00:00
+### 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/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/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/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/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
git://source.jalview.org / jabaws.git / blobdiff