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