2 ### Clustal configuration ###
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3 local.clustalw.bin.windows=binaries/windows/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/jaba2/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 ram=6000M
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15 ###### CLUSTAL OMEGA CONFIGURATION ######
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16 local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe
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17 local.clustalo.bin=binaries/src/clustalo/src/clustalo
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18 cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo
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19 ## This parameters specifies the directory where the matrices files are stored
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20 #clustalo.presets.file=conf/settings/ClustaloPresets.xml
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21 clustalo.parameters.file=conf/settings/ClustaloParameters.xml
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22 clustalo.limits.file=conf/settings/ClustaloLimits.xml
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23 ## ClustalO can be executed on multiple CPUs if run on the cluster.
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24 ## This parameter specifies the number of CPUs to use
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25 clustalo.cluster.cpunum=4
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26 ## This reserves a slot with CPUNUM on the cluster for the task
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27 clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00
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30 ### Muscle configuration ###
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31 local.muscle.bin.windows=binaries/windows/muscle.exe
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32 local.muscle.bin=binaries/src/muscle/muscle
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33 # Beware version of muscle on the cluster older and does not support some
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34 # of the newer version attributed thus, will not work with Muscle.java wrapper!
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35 cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle
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36 #The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored
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37 # e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!
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38 muscle.-matrix.path=binaries/matrices
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39 muscle.presets.file=conf/settings/MusclePresets.xml
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40 muscle.parameters.file=conf/settings/MuscleParameters.xml
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41 muscle.limits.file=conf/settings/MuscleLimits.xml
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42 muscle.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M
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44 ### Mafft configuration ###
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45 #local.mafft.bin.windows=
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46 local.mafft.bin=binaries/src/mafft/scripts/mafft
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47 cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft
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48 # These paths will be converted to absolute if relative.
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49 mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
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50 mafft.--aamatrix.path=binaries/matrices
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51 mafft.presets.file=conf/settings/MafftPresets.xml
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52 mafft.parameters.file=conf/settings/MafftParameters.xml
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53 mafft.limits.file=conf/settings/MafftLimits.xml
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54 mafft.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M
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57 ### Tcoffee configuration ###
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58 local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee
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59 cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee
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61 # Sub matrix support does not work
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62 #tcoffee.-matrix.path=binaries/matrices
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63 # This variable is required by tcoffee
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64 tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;
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65 tcoffee.presets.file=conf/settings/TcoffeePresets.xml
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66 tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml
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67 tcoffee.limits.file=conf/settings/TcoffeeLimits.xml
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68 tcoffee.cluster.cpunum=4
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69 tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00
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71 ### Probcons configuration ###
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72 #local.probcons.bin.windows=
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73 local.probcons.bin=binaries/src/probcons/probcons
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74 cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons
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75 #Probcons does not support matrix loading - unrecognised option reported!
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76 probcons.parameters.file=conf/settings/ProbconsParameters.xml
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77 probcons.limits.file=conf/settings/ProbconsLimits.xml
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78 probcons.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M
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80 ### Jronn configuration ###
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81 local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe
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82 local.jronn.bin=/sw/java/latest/bin/java
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83 cluster.jronn.bin=/sw/java/latest/bin/java
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84 jronn.jar.file=binaries/windows/jronn3.1.jar
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85 # jronn.parameters.file=conf/settings/JronnParameters.xml
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86 jronn.limits.file=conf/settings/JronnLimits.xml
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87 #TODO jronn.jvm.options=-Xms32M -Xmx512M
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88 jronn.cluster.cpunum=4
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89 jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00
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92 ### Disembl configuration Tisean - Disembl dependancy ###
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93 #local.disembl.bin.windows=
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94 local.disembl.bin=binaries/src/disembl/DisEMBL.py
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95 cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py
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96 # disembl.parameters.file=conf/settings/DisemblParameters.xml
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97 disembl.limits.file=conf/settings/DisemblLimits.xml
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98 disembl.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M
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100 ### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ###
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101 #local.disembl.bin.windows=
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102 local.globplot.bin=binaries/src/globplot/GlobPlot.py
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103 cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py
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104 # Dundee only settings
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105 globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50
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106 # globplot.parameters.file=conf/settings/GlobPlotParameters.xml
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107 globplot.limits.file=conf/settings/GlobPlotLimits.xml
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108 globplot.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M
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110 ### IUPred configuration ###
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111 local.iupred.bin.windows=binaries/windows/iupred/iupred.exe
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112 local.iupred.bin=binaries/src/iupred/iupred
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113 # This must point to the directory where iupred binary is, with other files it depends on
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114 #iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred
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115 # This path will be converted to absolute if relative.
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116 iupred.bin.env=IUPred_PATH#binaries/src/iupred
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117 cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred
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118 iupred.parameters.file=conf/settings/IUPredParameters.xml
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119 iupred.limits.file=conf/settings/IUPredLimits.xml
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120 iupred.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M
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122 ### AACon configuration ###
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123 # This is just a path to the standard java executable
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124 local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe
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125 local.aacon.bin=/sw/java/latest/bin/java
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126 cluster.aacon.bin=/sw/java/latest/bin/java
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127 # Path to the AACon library
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128 aacon.jar.file=binaries/windows/aaconservation.jar
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129 aacon.parameters.file=conf/settings/AAConParameters.xml
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130 aacon.presets.file=conf/settings/AAConPresets.xml
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131 aacon.limits.file=conf/settings/AAConLimits.xml
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132 aacon.cluster.cpunum=4
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133 aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=6000M -l h_cpu=24:00:00
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