dundee-conf/Executable.properties

   1 \r
   2 ### Clustal configuration ###\r
   3 local.clustalw.bin.windows=binaries/windows/clustalw2.exe\r
   4 local.clustalw.bin=binaries/src/clustalw/src/clustalw2\r
   5 cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2\r
   6 # Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison!\r
   7 # see engine.client.Util.getExecProperty() method for details  \r
   8 # So they are case insensitive. \r
   9 clustalw.-matrix.path=binaries/matrices\r
  10 clustalw.presets.file=conf/settings/ClustalPresets.xml\r
  11 clustalw.parameters.file=conf/settings/ClustalParameters.xml\r
  12 clustalw.limits.file=conf/settings/ClustalLimits.xml\r
  13 clustalw.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
  14 \r
  15 ######                 CLUSTAL OMEGA CONFIGURATION                ######\r
  16 local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe\r
  17 local.clustalo.bin=binaries/src/clustalo/src/clustalo\r
  18 cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo\r
  19 ## This parameters specifies the directory where the matrices files are stored   \r
  20 #clustalo.presets.file=conf/settings/ClustaloPresets.xml\r
  21 clustalo.parameters.file=conf/settings/ClustaloParameters.xml\r
  22 clustalo.limits.file=conf/settings/ClustaloLimits.xml\r
  23 ## ClustalO can be executed on multiple CPUs if run on the cluster. \r
  24 ## This parameter specifies the number of CPUs to use\r
  25 clustalo.cluster.cpunum=4\r
  26 ## This reserves a slot with CPUNUM on the cluster for the task\r
  27 clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00  \r
  28 \r
  29 \r
  30 ### Muscle configuration ###\r
  31 local.muscle.bin.windows=binaries/windows/muscle.exe\r
  32 local.muscle.bin=binaries/src/muscle/muscle\r
  33 # Beware version of muscle on the cluster older and does not support some \r
  34 # of the newer version attributed thus, will not work with Muscle.java wrapper!\r
  35 cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle\r
  36 #The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored\r
  37 # e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path!\r
  38 muscle.-matrix.path=binaries/matrices\r
  39 muscle.presets.file=conf/settings/MusclePresets.xml\r
  40 muscle.parameters.file=conf/settings/MuscleParameters.xml\r
  41 muscle.limits.file=conf/settings/MuscleLimits.xml\r
  42 muscle.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
  43 \r
  44 ### Mafft configuration ###\r
  45 #local.mafft.bin.windows=\r
  46 local.mafft.bin=binaries/src/mafft/scripts/mafft\r
  47 cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft\r
  48 # These paths will be converted to absolute if relative.\r
  49 mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
  50 mafft.--aamatrix.path=binaries/matrices\r
  51 mafft.presets.file=conf/settings/MafftPresets.xml\r
  52 mafft.parameters.file=conf/settings/MafftParameters.xml\r
  53 mafft.limits.file=conf/settings/MafftLimits.xml\r
  54 mafft.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
  55 \r
  56 \r
  57 ### Tcoffee configuration ###\r
  58 local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee\r
  59 cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
  60 #/sw/bin/t_coffee\r
  61 # Sub matrix support does not work \r
  62 #tcoffee.-matrix.path=binaries/matrices\r
  63 # This variable is required by tcoffee\r
  64 tcoffee.bin.env=HOME_4_TCOFFEE#jobsout;\r
  65 tcoffee.presets.file=conf/settings/TcoffeePresets.xml\r
  66 tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml\r
  67 tcoffee.limits.file=conf/settings/TcoffeeLimits.xml\r
  68 tcoffee.cluster.cpunum=4\r
  69 tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00  \r
  70 \r
  71 ### Probcons configuration ###\r
  72 #local.probcons.bin.windows=\r
  73 local.probcons.bin=binaries/src/probcons/probcons\r
  74 cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons\r
  75 #Probcons does not support matrix loading - unrecognised option reported! \r
  76 probcons.parameters.file=conf/settings/ProbconsParameters.xml\r
  77 probcons.limits.file=conf/settings/ProbconsLimits.xml\r
  78 probcons.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
  79 \r
  80 ### Jronn configuration ### \r
  81 local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
  82 local.jronn.bin=/sw/java/latest/bin/java\r
  83 cluster.jronn.bin=/sw/java/latest/bin/java\r
  84 jronn.jar.file=binaries/windows/jronn3.1.jar\r
  85 # jronn.parameters.file=conf/settings/JronnParameters.xml\r
  86 jronn.limits.file=conf/settings/JronnLimits.xml\r
  87 #TODO jronn.jvm.options=-Xms32M -Xmx512M\r
  88 jronn.cluster.cpunum=4\r
  89 jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=4000M -l h_cpu=24:00:00\r
  90 \r
  91 \r
  92 ### Disembl configuration Tisean - Disembl dependancy ### \r
  93 #local.disembl.bin.windows= \r
  94 local.disembl.bin=binaries/src/disembl/DisEMBL.py\r
  95 cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
  96 # disembl.parameters.file=conf/settings/DisemblParameters.xml\r
  97 disembl.limits.file=conf/settings/DisemblLimits.xml\r
  98 disembl.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
  99 \r
 100 ### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### \r
 101 #local.disembl.bin.windows= \r
 102 local.globplot.bin=binaries/src/globplot/GlobPlot.py\r
 103 cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py\r
 104 # Dundee only settings\r
 105 globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 \r
 106 # globplot.parameters.file=conf/settings/GlobPlotParameters.xml\r
 107 globplot.limits.file=conf/settings/GlobPlotLimits.xml\r
 108 globplot.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 109 \r
 110 ### IUPred configuration ### \r
 111 local.iupred.bin.windows=binaries/windows/iupred/iupred.exe \r
 112 local.iupred.bin=binaries/src/iupred/iupred\r
 113 # This must point to the directory where iupred binary is, with other files it depends on\r
 114 #iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred\r
 115 # This path will be converted to absolute if relative. \r
 116 iupred.bin.env=IUPred_PATH#binaries/src/iupred\r
 117 cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred\r
 118 iupred.parameters.file=conf/settings/IUPredParameters.xml\r
 119 iupred.limits.file=conf/settings/IUPredLimits.xml\r
 120 iupred.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 121 \r
 122 ### AACon configuration ###\r
 123 # This is just a path to the standard java executable \r
 124 local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
 125 local.aacon.bin=/sw/java/latest/bin/java\r
 126 cluster.aacon.bin=/sw/java/latest/bin/java\r
 127 # Path to the AACon library\r
 128 aacon.jar.file=binaries/windows/aaconservation.jar\r
 129 aacon.parameters.file=conf/settings/AAConParameters.xml\r
 130 aacon.presets.file=conf/settings/AAConPresets.xml\r
 131 aacon.limits.file=conf/settings/AAConLimits.xml\r
 132 aacon.cluster.cpunum=4\r
 133 aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=4000M -l h_cpu=24:00:00\r