### Clustal configuration ###
local.clustalw.bin.windows=binaries/clustalw2.exe
local.clustalw.bin=binaries/src/clustalw/src/clustalw2
#cluster.clustalw.bin=/homes/pvtroshin/workspace/clustengine/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 h_vmem=6000M -l ram=6000M

### Muscle configuration ###
local.muscle.bin.windows=binaries/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
#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

### 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
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

### 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
#/sw/bin/t_coffee
# Sub matrix support does not work 
#tcoffee.-matrix.path=binaries/matrices
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  

### Probcons configuration ###
#local.probcons.bin.windows=
local.probcons.bin=binaries/src/probcons/probcons
#cluster.probcons.bin=/homes/pvtroshin/workspace/clustengine/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