+################################################################################\r
+# THIS IS JABAWS EXECUTABLE CONFIGURATION FILE # \r
+################################################################################\r
+\r
+#File structure: \r
+\r
+# Uncomment this if you want to limit the size of the job to be accepted by a WS\r
+#clustalw.limits.file=conf/settings/ClustalLimits.xml\r
+\r
+# Uncomment this if you want to limit the size of the job to be accepted by a WS\r
+\r
+# Uncomment this if your what set a maximum execution time for this webservice \r
+# to 24 hours and maximum amount of memory per task to 6Gb. Please note that \r
+# you may need to change this if your cluster scheduler is not SGE or OGE. \r
+#mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+# The number of CPU to use on the cluster by a Tcoffee \r
+#tcoffee.cluster.cpunum=4\r
\r
### Clustal configuration ###\r
-local.clustalw.bin.windows=binaries/clustalw2.exe\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
+#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 h_vmem=6000M -l ram=6000M\r
+#clustalw.limits.file=conf/settings/ClustalLimits.xml\r
+#clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
\r
### Muscle configuration ###\r
-local.muscle.bin.windows=binaries/muscle.exe\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
+#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 h_vmem=6000M -l ram=6000M\r
+#muscle.limits.file=conf/settings/MuscleLimits.xml\r
+#muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
\r
### Mafft configuration ###\r
-#local.mafft.bin.windows=\r
-local.mafft.bin=binaries/src/mafft/binaries/mafft\r
-cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/core/mafft\r
+local.mafft.bin=binaries/src/mafft/scripts/mafft\r
+#cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/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 h_vmem=6000M -l ram=6000M\r
+#mafft.limits.file=conf/settings/MafftLimits.xml\r
+#mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -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
+#cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/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 h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 \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 h_vmem=1700M -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
+#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 h_vmem=6000M -l ram=6000M\r
-\r
-### Jronn configuration ### \r
-local.jronn.bin.windows=D:\\Java\\jdk1.6.0_14\\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/jronn3.1.jar\r
-jronn.parameters.file=conf/settings/JronnParameters.xml\r
+#probcons.limits.file=conf/settings/ProbconsLimits.xml\r
+#probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+### Jronn configuration ###\r
+# If no local path are specified, Java is loaded from JAVA_HOME environment \r
+# variable for local execution \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.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 h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r
+#jronn.cluster.cpunum=4\r
+#jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -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 h_vmem=6000M -l ram=6000M\r
+#cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
+#disembl.limits.file=conf/settings/DisemblLimits.xml\r
+#disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -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
-# globplot.parameters.file=conf/settings/GlobPlotParameters.xml\r
+#cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
+#globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/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 h_vmem=6000M -l ram=6000M\r
+#globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -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 h_vmem=6000M -l ram=6000M\r
\r
### AACon configuration ###\r
-local.aacon.bin.windows=D:\\Java\\jdk1.6.0_14\\bin\\java.exe \r
-local.aacon.bin=/sw/java/latest/bin/java\r
-cluster.aacon.bin=/sw/java/latest/bin/java\r
-aacon.jar.file=binaries/aaconservation.jar\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
-#TODO jronn.jvm.options=-Xms32M -Xmx512M\r
-aacon.cluster.cpunum=4\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 h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r
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