1 ###########################################################################################
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3 # THIS IS JABAWS EXECUTABLE CONFIGURATION FILE #
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5 ###########################################################################################
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7 ### Properties supported by executables.
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8 ### <execname> is one of the available applications:
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9 ### [clustalw, mafft, muscle, propcons, tcoffee, iupred, jronn, globplot, disembl, aacon, jpred]
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11 ### Path to the native executable on Windows must be either absolute,
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12 ### or relative to JABAWS web application
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13 # local.<execname>.bin.windows = binaries/windows/clustalw2.exe
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15 ### Path to the native executable not on Windows (e.g. Linux, Mac)
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16 ### must be either absolute, or relative to JABAWS web application
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17 # local.<execname>.bin = binaries/src/clustalw/src/clustalw2
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19 ### Path to the native executable on the cluster (must be accessible from all
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20 ### cluster nodes which will run JABAWS jobs). The path must be absolute.
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21 # cluster.<execname>.bin = /home/jabaws/binaries/src/clustalw/src/clustalw2
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23 ### At least one of the path to the native executable should be defined.
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25 ### If an application supports presets, the preset file can have either
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26 ### absolute or relative to the JABAWS web application path to the file.
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27 ### The file is optional.
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28 # <execname>.presets.file = conf/settings/ClustalPresets.xml
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30 ### If an application supports parameters, the parameter file can have either
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31 ### absolute or relative to the JABAWS web application path to the file.
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32 ### The file is optional.
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33 # <execname>.parameters.file = conf/settings/ClustalParameters.xml
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35 ## Application limits, absolute or relative to
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36 ## the JABAWS web application path to the file. Optional.
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37 ## Use this if you want to limit the size of the job to be accepted by a
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38 ## Webservice. The limits files we use in Dundee are provided with JABAWS.
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39 # <execname>.limits.file=conf/settings/ClustalLimits.xml
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41 ## Flags passed to the cluster batch manager for the application. Optional.
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42 ## This example sets a maximum execution time to 24 hours and maximum amount of
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43 ## memory per task to 6Gb for SGE and OGE cluster batch managers.
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44 ## Please note that all the examples of this parameter below are correct for
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45 ## Sun Grid Engine or Open Grid Engine (untested) only! If you use a different
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46 ## batch manager you would need to specify different flags.
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47 # <execname>.cluster.settings = -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
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49 ## Environmental variables required by native executables. Optional.
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50 ## Format: VARIABLE_NAME1#VARIABLE_VALUE1;VARIABLE_NAME2#VARIABLE_VALUE2;
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51 # <execname>.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
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53 ## Parameter supported by the executable Jar files, such as jronn and aacon,
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54 ## point to the location of the jar file. Also, local.<execname>.bin,
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55 ## local.<execname>.bin.windows properties are optional for these, if not
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56 ## provided they will be replaced to the java executable path from JAVA_HOME
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57 ## environmental variable.
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58 #<execname>.jar.file = binaries/windows/bj3.0.4p-jronn.jar
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63 ###########################################################################################
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64 # CLUSTAL W CONFIGURATION #
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65 ###########################################################################################
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66 local.clustalw.bin.windows = binaries/windows/clustalw2.exe
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67 local.clustalw.bin = binaries/src/clustalw/src/clustalw2
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68 #cluster.clustalw.bin =/home/jabaws/binaries/src/clustalw/src/clustalw2
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69 ### This parameter specifies the directory where the matrices files are stored
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70 clustalw.-matrix.path = binaries/matrices
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71 clustalw.presets.file = conf/settings/ClustalPresets.xml
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72 clustalw.parameters.file = conf/settings/ClustalParameters.xml
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73 clustalw.limits.file = conf/settings/ClustalLimits.xml
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74 #clustalw.cluster.settings =-l h_cpu=24:00:00 -l ram=6000M
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77 ###########################################################################################
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78 # CLUSTAL OMEGA CONFIGURATION #
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79 ###########################################################################################
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80 local.clustalo.bin.windows = binaries/windows/clustalo/clustalo.exe
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81 local.clustalo.bin = binaries/src/clustalo/src/clustalo
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82 #cluster.clustalo.bin = /home/jabaws/binaries/src/clustalo/src/clustalo
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83 ### This parameter specifies the directory where the matrices files are stored
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84 #clustalo.presets.file = conf/settings/ClustaloPresets.xml
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85 clustalo.parameters.file = conf/settings/ClustaloParameters.xml
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86 clustalo.limits.file = conf/settings/ClustaloLimits.xml
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87 ### ClustalO can be run on multiple CPUs on the cluster. This parameter specifies CPU #NN
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88 clustalo.cluster.cpunum = 4
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89 ### This reserves a slot with CPUNUM on the cluster for the task
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90 #clustalo.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00
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93 ###########################################################################################
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94 # MUSCLE CONFIGURATION #
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95 ###########################################################################################
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96 local.muscle.bin.windows = binaries/windows/muscle.exe
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97 local.muscle.bin = binaries/src/muscle/muscle
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98 #cluster.muscle.bin = /home/jabaws/binaries/src/muscle/muscle
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99 ### This parameter specifies the directory where the matrices files are stored
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100 muscle.-matrix.path = binaries/matrices
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101 muscle.presets.file = conf/settings/MusclePresets.xml
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102 muscle.parameters.file = conf/settings/MuscleParameters.xml
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103 muscle.limits.file = conf/settings/MuscleLimits.xml
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104 #muscle.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M
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107 ###########################################################################################
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108 # MAFFT CONFIGURATION #
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109 ###########################################################################################
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110 local.mafft.bin = binaries/src/mafft/scripts/mafft
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111 #cluster.mafft.bin = /home/jabaws/binaries/src/mafft/scripts/mafft
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112 # These paths will be converted to absolute if relative.
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113 mafft.bin.env = MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
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114 ### This parameters specifies the directory where the matrices files are stored
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115 mafft.--aamatrix.path = binaries/matrices
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116 mafft.presets.file = conf/settings/MafftPresets.xml
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117 mafft.parameters.file = conf/settings/MafftParameters.xml
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118 mafft.limits.file = conf/settings/MafftLimits.xml
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119 #mafft.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M
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122 ###########################################################################################
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123 # TCOFFEE CONFIGURATION #
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124 ###########################################################################################
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125 local.tcoffee.bin = binaries/src/tcoffee/t_coffee_source/t_coffee
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126 #cluster.tcoffee.bin = /home/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee
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127 # This variable is required by tcoffee
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128 tcoffee.bin.env = HOME_4_TCOFFEE#jobsout;
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129 tcoffee.presets.file = conf/settings/TcoffeePresets.xml
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130 tcoffee.parameters.file = conf/settings/TcoffeeParameters.xml
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131 tcoffee.limits.file = conf/settings/TcoffeeLimits.xml
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132 ### Tcoffee can be executed on multiple CPUs if run on the cluster. This parameter defines CPUs #N
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133 #tcoffee.cluster.cpunum = 4
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134 ### This paramer defines queue setting with CPUNUM on the cluster
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135 #tcoffee.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00
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138 ###########################################################################################
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139 # PROBCONS CONFIGURATION #
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140 ###########################################################################################
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141 local.probcons.bin = binaries/src/probcons/probcons
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142 #cluster.probcons.bin = /home/jabaws/binaries/src/probcons/probcons
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143 probcons.parameters.file = conf/settings/ProbconsParameters.xml
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144 probcons.limits.file = conf/settings/ProbconsLimits.xml
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145 ### This parameter defines queue settings for PROBCON on the cluster
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146 #probcons.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M
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149 ###########################################################################################
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150 # JRONN CONFIGURATION #
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151 ###########################################################################################
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152 ### If no local path is specified, Java is loaded from JAVA_HOME variable for local
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153 ### execution. However, cluster.jronn.bin MUST be specified for running Jronn on the cluster.
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154 #local.jronn.bin.windows = D:\\Java\\jdk1.6.0_24\\bin\\java.exe
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155 #local.jronn.bin = /sw/java/latest/bin/java
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156 #cluster.jronn.bin = /sw/java/latest/bin/java
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157 jronn.jar.file = binaries/windows/bj3.0.4p-jronn.jar
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158 jronn.limits.file = conf/settings/JronnLimits.xml
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159 ## Jronn can use multiple CPUs. This parameter specifies the number of CPUs
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160 #jronn.cluster.cpunum = 4
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161 ### This reserves a slot with CPUNUM on the cluster for the task
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162 #jronn.cluster.settings = -q 64bit-pri.q -pe smp 4 -l h_cpu=24:00:00
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165 ###########################################################################################
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166 # DISEMBL CONFIGURATION #
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167 ###########################################################################################
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168 local.disembl.bin = binaries/src/disembl/DisEMBL.py
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169 #cluster.disembl.bin = /home/jabaws/binaries/src/disembl/DisEMBL.py
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170 disembl.limits.file = conf/settings/DisemblLimits.xml
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171 #disembl.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M
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174 ###########################################################################################
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175 # GLOBPLOT CONFIGURATION #
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176 ###########################################################################################
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177 local.globplot.bin = binaries/src/globplot/GlobPlot.py
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178 #cluster.globplot.bin = /home/jabaws/binaries/src/globplot/GlobPlot.py
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179 #globplot.bin.env = PYTHONPATH#/home/jabaws/binaries/src/globplot/biopython-1.50
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180 globplot.limits.file = conf/settings/GlobPlotLimits.xml
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181 #globplot.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M
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184 ###########################################################################################
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185 # IUPRED CONFIGURATION #
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186 ###########################################################################################
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187 local.iupred.bin.windows = binaries/windows/iupred/iupred.exe
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188 local.iupred.bin = binaries/src/iupred/iupred
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189 ### This must point to the directory where iupred binary is, with other files it
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190 ### depends on. This path will be converted to absolute if relative at runtime.
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191 iupred.bin.env = IUPred_PATH#binaries/src/iupred
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192 #cluster.iupred.bin = /home/jabaws/binaries/src/iupred/iupred
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193 iupred.parameters.file = conf/settings/IUPredParameters.xml
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194 iupred.limits.file = conf/settings/IUPredLimits.xml
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195 #iupred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M
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198 ###########################################################################################
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199 # AACON CONFIGURATION #
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200 ###########################################################################################
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201 ### This is just a path to the standard java executable
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202 #local.aacon.bin.windows = D:\\Java\\jdk1.6.0_24\\bin\\java.exe
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203 #local.aacon.bin = /sw/java/latest/bin/java
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204 #cluster.aacon.bin = /sw/java/latest/bin/java
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205 ### Path to the AACon library
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206 aacon.jar.file = binaries/windows/aaconservation.jar
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207 aacon.parameters.file = conf/settings/AAConParameters.xml
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208 aacon.presets.file = conf/settings/AAConPresets.xml
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209 aacon.limits.file = conf/settings/AAConLimits.xml
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210 ### AACon can use multiple CPUs. This parameter defines the number of CPUs:
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211 #aacon.cluster.cpunum = 4
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212 ### This parameter defines queue settings for AACON on the cluster
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213 #aacon.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00
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215 ###########################################################################################
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216 # JPRED CONFIGURATION #
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217 ###########################################################################################
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218 local.jpred.bin = binaries/src/jpred/jpred.pl
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219 #cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl
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220 # These paths will be converted to absolute if relative.
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221 jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast;UNIREFDB#binaries/src/jpred/unirefdb;
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222 ### This parameters specifies the directory where the matrices files are stored
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223 jpred.presets.file = conf/settings/JpredPresets.xml
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224 jpred.parameters.file = conf/settings/JpredParameters.xml
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225 jpred.limits.file = conf/settings/JpredLimits.xml
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226 jpred.cluster.cpunum = 4
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227 #jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M
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