X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=caf735577f5f0c78f7855b884cb5bdfcad603ce7;hb=550d715f5af9271247b20363d1212e7e0279f9ee;hp=681b3f0cfdf809adb47d553b95a0cc08bf7c4c86;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 681b3f0..caf7355 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -1,8 +1,8 @@
 
 ### Clustal configuration ###
-local.clustalw.bin.windows=binaries/clustalw2.exe
+local.clustalw.bin.windows=binaries/windows/clustalw2.exe
 local.clustalw.bin=binaries/src/clustalw/src/clustalw2
-#cluster.clustalw.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/src/clustalw2
+cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2
 # Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!
 # see engine.client.Util.getExecProperty() method for details  
 # So they are case insensitive. 
@@ -10,50 +10,109 @@ clustalw.-matrix.path=binaries/matrices
 clustalw.presets.file=conf/settings/ClustalPresets.xml
 clustalw.parameters.file=conf/settings/ClustalParameters.xml
 clustalw.limits.file=conf/settings/ClustalLimits.xml
-#clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 
 ### Muscle configuration ###
-local.muscle.bin.windows=binaries/muscle.exe
+local.muscle.bin.windows=binaries/windows/muscle.exe
 local.muscle.bin=binaries/src/muscle/muscle
 # Beware version of muscle on the cluster older and does not support some 
 # of the newer version attributed thus, will not work with Muscle.java wrapper!
-cluster.muscle.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/muscle/muscle
+cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle
 #The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored
 # e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!
 muscle.-matrix.path=binaries/matrices
 muscle.presets.file=conf/settings/MusclePresets.xml
 muscle.parameters.file=conf/settings/MuscleParameters.xml
 muscle.limits.file=conf/settings/MuscleLimits.xml
-#muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 
 ### Mafft configuration ###
 #local.mafft.bin.windows=
-local.mafft.bin=binaries/src/mafft/binaries/mafft
-#cluster.mafft.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/mafft/core/mafft
+local.mafft.bin=binaries/src/mafft/scripts/mafft
+cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft
+# These paths will be converted to absolute if relative.
 mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
 mafft.--aamatrix.path=binaries/matrices
 mafft.presets.file=conf/settings/MafftPresets.xml
 mafft.parameters.file=conf/settings/MafftParameters.xml
 mafft.limits.file=conf/settings/MafftLimits.xml
-#mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+
 
 ### Tcoffee configuration ###
 local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee
-#cluster.tcoffee.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/tcoffee/t_coffee_source/t_coffee
+cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee
 #/sw/bin/t_coffee
 # Sub matrix support does not work 
 #tcoffee.-matrix.path=binaries/matrices
+# This variable is required by tcoffee
+tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;
 tcoffee.presets.file=conf/settings/TcoffeePresets.xml
 tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml
 tcoffee.limits.file=conf/settings/TcoffeeLimits.xml
-#tcoffee.cluster.cpunum=4
-#tcoffee.cluster.settings=-q mpi -pe mpi 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  
+tcoffee.cluster.cpunum=4
+tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  
 
 ### Probcons configuration ###
 #local.probcons.bin.windows=
 local.probcons.bin=binaries/src/probcons/probcons
-#cluster.probcons.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/probcons/probcons
+cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons
 #Probcons does not support matrix loading - unrecognised option reported! 
 probcons.parameters.file=conf/settings/ProbconsParameters.xml
 probcons.limits.file=conf/settings/ProbconsLimits.xml
-#probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+
+### Jronn configuration ### 
+local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe 
+local.jronn.bin=/sw/java/latest/bin/java
+cluster.jronn.bin=/sw/java/latest/bin/java
+jronn.jar.file=binaries/windows/jronn3.1.jar
+# jronn.parameters.file=conf/settings/JronnParameters.xml
+jronn.limits.file=conf/settings/JronnLimits.xml
+#TODO jronn.jvm.options=-Xms32M -Xmx512M
+jronn.cluster.cpunum=4
+jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00
+
+
+### Disembl configuration Tisean - Disembl dependancy ### 
+#local.disembl.bin.windows= 
+local.disembl.bin=binaries/src/disembl/DisEMBL.py
+cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py
+# disembl.parameters.file=conf/settings/DisemblParameters.xml
+disembl.limits.file=conf/settings/DisemblLimits.xml
+disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+
+### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### 
+#local.disembl.bin.windows= 
+local.globplot.bin=binaries/src/globplot/GlobPlot.py
+cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py
+# Dundee only settings
+globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 
+# globplot.parameters.file=conf/settings/GlobPlotParameters.xml
+globplot.limits.file=conf/settings/GlobPlotLimits.xml
+globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+
+### IUPred configuration ### 
+local.iupred.bin.windows=binaries/windows/iupred/iupred.exe 
+local.iupred.bin=binaries/src/iupred/iupred
+# This must point to the directory where iupred binary is, with other files it depends on
+#iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred
+# This path will be converted to absolute if relative. 
+iupred.bin.env=IUPred_PATH#binaries/src/iupred
+cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred
+iupred.parameters.file=conf/settings/IUPredParameters.xml
+iupred.limits.file=conf/settings/IUPredLimits.xml
+iupred.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
+
+### AACon configuration ###
+# This is just a path to the standard java executable 
+local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe 
+local.aacon.bin=/sw/java/latest/bin/java
+cluster.aacon.bin=/sw/java/latest/bin/java
+# Path to the AACon library
+aacon.jar.file=binaries/windows/aaconservation.jar
+aacon.parameters.file=conf/settings/AAConParameters.xml
+aacon.presets.file=conf/settings/AAConPresets.xml
+aacon.limits.file=conf/settings/AAConLimits.xml
+#TODO jronn.jvm.options=-Xms32M -Xmx512M
+aacon.cluster.cpunum=4