1 ################################################################################
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2 # THIS IS JABAWS EXECUTABLE CONFIGURATION FILE #
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3 ################################################################################
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7 # Uncomment this if you want to limit the size of the job to be accepted by a WS
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8 #clustalw.limits.file=conf/settings/ClustalLimits.xml
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10 # Uncomment this if you want to limit the size of the job to be accepted by a WS
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12 # Uncomment this if your what set a maximum execution time for this webservice
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13 # to 24 hours and maximum amount of memory per task to 6Gb. Please note that
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14 # you may need to change this if your cluster scheduler is not SGE or OGE.
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15 #mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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17 # The number of CPU to use on the cluster by a Tcoffee
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18 #tcoffee.cluster.cpunum=4
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20 ### Clustal configuration ###
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21 local.clustalw.bin.windows=binaries/windows/clustalw2.exe
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22 local.clustalw.bin=binaries/src/clustalw/src/clustalw2
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23 cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2
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24 # Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!
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25 # see engine.client.Util.getExecProperty() method for details
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26 # So they are case insensitive.
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27 clustalw.-matrix.path=binaries/matrices
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28 clustalw.presets.file=conf/settings/ClustalPresets.xml
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29 clustalw.parameters.file=conf/settings/ClustalParameters.xml
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30 #clustalw.limits.file=conf/settings/ClustalLimits.xml
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31 #clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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33 ### Muscle configuration ###
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34 local.muscle.bin.windows=binaries/windows/muscle.exe
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35 local.muscle.bin=binaries/src/muscle/muscle
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36 cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle
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37 #The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored
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38 # e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!
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39 muscle.-matrix.path=binaries/matrices
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40 muscle.presets.file=conf/settings/MusclePresets.xml
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41 muscle.parameters.file=conf/settings/MuscleParameters.xml
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42 #muscle.limits.file=conf/settings/MuscleLimits.xml
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43 #muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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45 ### Mafft configuration ###
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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 h_vmem=6000M -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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60 # This variable is required by tcoffee
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61 tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;
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62 tcoffee.presets.file=conf/settings/TcoffeePresets.xml
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63 tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml
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64 #tcoffee.limits.file=conf/settings/TcoffeeLimits.xml
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65 #tcoffee.cluster.cpunum=4
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66 #tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00
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68 ### Probcons configuration ###
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69 local.probcons.bin=binaries/src/probcons/probcons
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70 cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons
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71 #Probcons does not support matrix loading - unrecognised option reported!
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72 probcons.parameters.file=conf/settings/ProbconsParameters.xml
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73 #probcons.limits.file=conf/settings/ProbconsLimits.xml
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74 #probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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76 ### Jronn configuration ###
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77 local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe
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78 local.jronn.bin=/sw/java/latest/bin/java
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79 cluster.jronn.bin=/sw/java/latest/bin/java
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80 jronn.jar.file=binaries/windows/jronn3.1.jar
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81 jronn.limits.file=conf/settings/JronnLimits.xml
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82 #jronn.cluster.cpunum=4
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83 #jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00
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86 ### Disembl configuration Tisean - Disembl dependancy ###
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87 local.disembl.bin=binaries/src/disembl/DisEMBL.py
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88 cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py
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89 #disembl.limits.file=conf/settings/DisemblLimits.xml
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90 #disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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92 ### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ###
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93 local.globplot.bin=binaries/src/globplot/GlobPlot.py
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94 cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py
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95 #globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50
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96 globplot.limits.file=conf/settings/GlobPlotLimits.xml
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97 #globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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99 ### IUPred configuration ###
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100 local.iupred.bin.windows=binaries/windows/iupred/iupred.exe
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101 local.iupred.bin=binaries/src/iupred/iupred
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102 # This must point to the directory where iupred binary is, with other files it depends on
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103 #iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred
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104 # This path will be converted to absolute if relative.
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105 iupred.bin.env=IUPred_PATH#binaries/src/iupred
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106 cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred
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107 iupred.parameters.file=conf/settings/IUPredParameters.xml
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108 #iupred.limits.file=conf/settings/IUPredLimits.xml
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109 #iupred.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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111 ### AACon configuration ###
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112 # This is just a path to the standard java executable
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113 local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe
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114 local.aacon.bin=/sw/java/latest/bin/java
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115 cluster.aacon.bin=/sw/java/latest/bin/java
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116 # Path to the AACon library
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117 aacon.jar.file=binaries/windows/aaconservation.jar
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118 aacon.parameters.file=conf/settings/AAConParameters.xml
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119 aacon.presets.file=conf/settings/AAConPresets.xml
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120 #aacon.limits.file=conf/settings/AAConLimits.xml
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121 #aacon.cluster.cpunum=4
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