dundee-conf/Executable.properties

   1 \r
   2 ### Clustal configuration ###\r
   3 local.clustalw.bin.windows=binaries/clustalw2.exe\r
   4 local.clustalw.bin=binaries/src/clustalw/src/clustalw2\r
   5 cluster.clustalw.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/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/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/www-jws2/servers/tomcat-jaba/webapps/jabaws/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/binaries/mafft\r
  32 cluster.mafft.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/mafft/binaries/mafft\r
  33 mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#/sw/bin/fasta34;\r
  34 mafft.--aamatrix.path=binaries/matrices\r
  35 mafft.presets.file=conf/settings/MafftPresets.xml\r
  36 mafft.parameters.file=conf/settings/MafftParameters.xml\r
  37 mafft.limits.file=conf/settings/MafftLimits.xml\r
  38 mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
  39 \r
  40 ### Tcoffee configuration ###\r
  41 local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee\r
  42 cluster.tcoffee.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee\r
  43 #/sw/bin/t_coffee\r
  44 # Sub matrix support does not work \r
  45 #tcoffee.-matrix.path=binaries/matrices\r
  46 tcoffee.presets.file=conf/settings/TcoffeePresets.xml\r
  47 tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml\r
  48 tcoffee.limits.file=conf/settings/TcoffeeLimits.xml\r
  49 tcoffee.cluster.cpunum=4\r
  50 tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  \r
  51 \r
  52 ### Probcons configuration ###\r
  53 #local.probcons.bin.windows=\r
  54 local.probcons.bin=binaries/src/probcons/probcons\r
  55 cluster.probcons.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/probcons/probcons\r
  56 #Probcons does not support matrix loading - unrecognised option reported! \r
  57 probcons.parameters.file=conf/settings/ProbconsParameters.xml\r
  58 probcons.limits.file=conf/settings/ProbconsLimits.xml\r
  59 probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r