conf/Executable.properties

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