### Clustal configuration ###
local.clustalw.bin.windows=binaries/windows/clustalw2.exe
local.clustalw.bin=binaries/src/clustalw/src/clustalw2
cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2
# Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!
# see engine.client.Util.getExecProperty() method for details  
# So they are case insensitive. 
clustalw.-matrix.path=binaries/matrices
clustalw.presets.file=conf/settings/ClustalPresets.xml
clustalw.parameters.file=conf/settings/ClustalParameters.xml
clustalw.limits.file=conf/settings/ClustalLimits.xml
clustalw.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M

######                 CLUSTAL OMEGA CONFIGURATION                ######
local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe
local.clustalo.bin=binaries/src/clustalo/src/clustalo
cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo
## This parameters specifies the directory where the matrices files are stored   
#clustalo.presets.file=conf/settings/ClustaloPresets.xml
clustalo.parameters.file=conf/settings/ClustaloParameters.xml
clustalo.limits.file=conf/settings/ClustaloLimits.xml
## ClustalO can be executed on multiple CPUs if run on the cluster. 
## This parameter specifies the number of CPUs to use
clustalo.cluster.cpunum=4
## This reserves a slot with CPUNUM on the cluster for the task
clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00  


### Muscle configuration ###
local.muscle.bin.windows=binaries/windows/muscle.exe
local.muscle.bin=binaries/src/muscle/muscle
# Beware version of muscle on the cluster older and does not support some 
# of the newer version attributed thus, will not work with Muscle.java wrapper!
cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle
#The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored
# e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!
muscle.-matrix.path=binaries/matrices
muscle.presets.file=conf/settings/MusclePresets.xml
muscle.parameters.file=conf/settings/MuscleParameters.xml
muscle.limits.file=conf/settings/MuscleLimits.xml
muscle.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M

### Mafft configuration ###
#local.mafft.bin.windows=
local.mafft.bin=binaries/src/mafft/scripts/mafft
cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft
# These paths will be converted to absolute if relative.
mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
mafft.--aamatrix.path=binaries/matrices
mafft.presets.file=conf/settings/MafftPresets.xml
mafft.parameters.file=conf/settings/MafftParameters.xml
mafft.limits.file=conf/settings/MafftLimits.xml
mafft.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M


### Tcoffee configuration ###
local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee
cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee
#/sw/bin/t_coffee
# Sub matrix support does not work 
#tcoffee.-matrix.path=binaries/matrices
# This variable is required by tcoffee
tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;
tcoffee.presets.file=conf/settings/TcoffeePresets.xml
tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml
tcoffee.limits.file=conf/settings/TcoffeeLimits.xml
tcoffee.cluster.cpunum=4
tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00  

### Probcons configuration ###
#local.probcons.bin.windows=
local.probcons.bin=binaries/src/probcons/probcons
cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons
#Probcons does not support matrix loading - unrecognised option reported! 
probcons.parameters.file=conf/settings/ProbconsParameters.xml
probcons.limits.file=conf/settings/ProbconsLimits.xml
probcons.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M

### Jronn configuration ### 
local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe 
local.jronn.bin=/sw/java/latest/bin/java
cluster.jronn.bin=/sw/java/latest/bin/java
jronn.jar.file=binaries/windows/jronn3.1.jar
# jronn.parameters.file=conf/settings/JronnParameters.xml
jronn.limits.file=conf/settings/JronnLimits.xml
#TODO jronn.jvm.options=-Xms32M -Xmx512M
jronn.cluster.cpunum=4
jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00


### Disembl configuration Tisean - Disembl dependancy ### 
#local.disembl.bin.windows= 
local.disembl.bin=binaries/src/disembl/DisEMBL.py
cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py
# disembl.parameters.file=conf/settings/DisemblParameters.xml
disembl.limits.file=conf/settings/DisemblLimits.xml
disembl.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M

### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### 
#local.disembl.bin.windows= 
local.globplot.bin=binaries/src/globplot/GlobPlot.py
cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py
# Dundee only settings
globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 
# globplot.parameters.file=conf/settings/GlobPlotParameters.xml
globplot.limits.file=conf/settings/GlobPlotLimits.xml
globplot.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M

### IUPred configuration ### 
local.iupred.bin.windows=binaries/windows/iupred/iupred.exe 
local.iupred.bin=binaries/src/iupred/iupred
# This must point to the directory where iupred binary is, with other files it depends on
#iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred
# This path will be converted to absolute if relative. 
iupred.bin.env=IUPred_PATH#binaries/src/iupred
cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred
iupred.parameters.file=conf/settings/IUPredParameters.xml
iupred.limits.file=conf/settings/IUPredLimits.xml
iupred.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M

### AACon configuration ###
# This is just a path to the standard java executable 
local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe 
local.aacon.bin=/sw/java/latest/bin/java
cluster.aacon.bin=/sw/java/latest/bin/java
# Path to the AACon library
aacon.jar.file=binaries/windows/aaconservation.jar
aacon.parameters.file=conf/settings/AAConParameters.xml
aacon.presets.file=conf/settings/AAConPresets.xml
aacon.limits.file=conf/settings/AAConLimits.xml
aacon.cluster.cpunum=4
aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00