2 ### Clustal configuration ###
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3 local.clustalw.bin.windows=binaries/clustalw2.exe
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4 local.clustalw.bin=binaries/src/clustalw/src/clustalw2
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5 #cluster.clustalw.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/src/clustalw2
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6 # Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!
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7 # see engine.client.Util.getExecProperty() method for details
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8 # So they are case insensitive.
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9 clustalw.-matrix.path=binaries/matrices
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10 clustalw.presets.file=conf/settings/ClustalPresets.xml
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11 clustalw.parameters.file=conf/settings/ClustalParameters.xml
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12 clustalw.limits.file=conf/settings/ClustalLimits.xml
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13 #clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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15 ### Muscle configuration ###
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16 local.muscle.bin.windows=binaries/muscle.exe
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17 local.muscle.bin=binaries/src/muscle/muscle
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18 # Beware version of muscle on the cluster older and does not support some
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19 # of the newer version attributed thus, will not work with Muscle.java wrapper!
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20 cluster.muscle.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/muscle/muscle
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21 #The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored
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22 # e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!
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23 muscle.-matrix.path=binaries/matrices
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24 muscle.presets.file=conf/settings/MusclePresets.xml
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25 muscle.parameters.file=conf/settings/MuscleParameters.xml
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26 muscle.limits.file=conf/settings/MuscleLimits.xml
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27 #muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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29 ### Mafft configuration ###
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30 #local.mafft.bin.windows=
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31 local.mafft.bin=binaries/src/mafft/binaries/mafft
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32 #cluster.mafft.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/mafft/core/mafft
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33 mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
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34 mafft.--aamatrix.path=binaries/matrices
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35 mafft.presets.file=conf/settings/MafftPresets.xml
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36 mafft.parameters.file=conf/settings/MafftParameters.xml
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37 mafft.limits.file=conf/settings/MafftLimits.xml
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38 #mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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40 ### Tcoffee configuration ###
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41 local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee
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42 #cluster.tcoffee.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/tcoffee/t_coffee_source/t_coffee
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44 # Sub matrix support does not work
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45 #tcoffee.-matrix.path=binaries/matrices
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46 tcoffee.presets.file=conf/settings/TcoffeePresets.xml
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47 tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml
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48 tcoffee.limits.file=conf/settings/TcoffeeLimits.xml
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49 #tcoffee.cluster.cpunum=4
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50 #tcoffee.cluster.settings=-q mpi -pe mpi 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00
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52 ### Probcons configuration ###
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53 #local.probcons.bin.windows=
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54 local.probcons.bin=binaries/src/probcons/probcons
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55 #cluster.probcons.bin=/homes/pvtroshin/workspace/clustengine/binaries/src/probcons/probcons
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56 #Probcons does not support matrix loading - unrecognised option reported!
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57 probcons.parameters.file=conf/settings/ProbconsParameters.xml
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58 probcons.limits.file=conf/settings/ProbconsLimits.xml
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59 #probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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